scaf4a (scaf4,LOC107555128)


Basic Information

Item Value
gene id scaf4a
gene name scaf4,LOC107555128
gene type misc
species striped catfish (Pangasianodon hypophthalmus)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_047611.1
NCBI id CM018557.1
chromosome length 24879021
location 10865612 ~ 10882265 (+)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome

Sequence

>TU316348
ctaatcAGAAGCGTGTATCTGTGTGATCTTTTGCTAAAAACTATAGGAATACAGTCTAGAGTGGGACCGATATGATCACATTGCATGGGCTTAGATGTGATGGAAACGATCCCATAtgtaaagaggaaaaaaaaaacacatatcaTTCTTACTGTTAAGGCCAGGCCAGTGCCCTGTGTGCACTGATTTAAAATAAGCTTACTCCATGTCCATACCCATGCAGATTTTGGGCACTACATGCTAATGTGCAGAAATGATTCAGAAACATGCTTCATTCTTAAGCTCTGAGGTTTAATTCTAATTTTAATGCCTGGTCTTCCTCCAATGATTTCATTGACTTACAACGCAATTGACGTCAAGTGTCTGGCTAACATGGAGCACCGTCCTGTGAATCAGTGTCCATTATTGAGTTTAAATGTTGTACTAAGCCAGTGTTTCATATCCCTGTACTGCACATTTTGGTGGTTTTCCTGCTTTAACATGCCCatgtaaaaaaatcatgaagGGCTTCTTAATAGTTAATGAATTGAGTCAGGCATGTTGGGACTAGGGGCCAAGCTAGAATGGACAGTGCAGGACTATCCCATGAGTAagattggagaaaaaaaactgttttttaaacaaaaagacatggaaaaaatggaaaataactCTGCTGTAAATATGCTTAcatctaataatatttgtaGAGTTGGAAGTTTTTCTGAAGTATACTTCTGTCAGTGTCACCAATGGATCCTTGACTAAAATAAGAGACAAAGCCCCGTttgctgtaatgtttttaacctaCAGTGTTTACATTGTACCAGAGATGAGAtgtttgtataatttttaaGTTTGTGCAGATGTGAACTCATTTAATATTTCAGCAATGGGGATTCAGTTTTAATAAACTATTTTCATACCAAAATGAAAAAACTGAATTCACAATATGACTTGTGTTGACGTCAGCAATgttagcttttttatttttattattattattattattattattattattattaaactaacCCTTGTATGCTTTATAGTGTGTCAAATAGGAAGCTGTTTTGGATCAGCCCTCATTTGCTTGTGCTGTATTTAAATTGGAGTTGCAAAAAAGGGCACAACTGTAAAAGGTTATGATTGGAAGCAGATTctgaacaataaaaaaaat
>TU316349
ctaatcAGAAGCGTGTATCTGTGTGATCTTTTGCTAAAAACTATAGGAATACAGTCTAGAGTGGGACCGATATGATCACATTGCATGGGCTTAGATGTGATGGAAACGATCCCATAtgtaaagaggaaaaaaaaaacacatatcaTTCTTACTGTTAAGGCCAGGCCAGTGCCCTGTGTGCACTGATTTAAAATAAGCTTACTCCATGTCCATACCCATGCAGATTTTGGGCACTACATGCTAATGTGCAGAAATGATTCAGAAACATGCTTCATTCTTAAGCTCTGAGGTTTAATTCTAATTTTAATGCCTGGTCTTCCTCCAATGATTTCATTGACTTACAACGCAATTGACGTCAAGTGTCTGGCTAACATGGAGCACCGTCCTGTGAATCAGTGTCCATTATTGAGTTTAAATGTTGTACTAAGCCAGTGTTTCATATCCCTGTACTGCACATTTTGGTGGTTTTCCTGCTTTAACATGCCCatgtaaaaaaatcatgaagGGCTTCTTAATAGTTAATGAATTGAGTCAGGCATGTTGGGACTAGGGGCCAAGCTAGAATGGACAGTGCAGGACTATCCCATGAGTAagattggagaaaaaaaactgttttttaaacaaaaagacatggaaaaaatggaaaataactCTGCTGTAAATATGCTTAcatctaataatatttgtaGAGTTGGAAGTTTTTCTGAAGTATACTTCTGTCAGTGTCACCAATGGATCCTTGACTAAAATAAGAGACAAAGCCCCGTttgctgtaatgtttttaacctaCAGTGTTTACATTGTACCAGAGATGAGAtgtttgtataatttttaaGTTTGTGCAGATGTGAACTCATTTAATATTTCAGCAATGGGGATTCAGTTTTAATAAACTATTTTCATACCAAAATGAAAAAACTGAATTCACAATATGACTTGTGTTGACGTCA
>XM_026941952.2
GAGAAACACGTGCAGCAATCCCAGCATGCCTCGCGCGCCGCAACGACTCCGCTCCTGTCTTCTTACTGAGGGCGAGAGGCGGCGGACATGTTGGGATGGCCCGTTAAGCCACACTACTTCATTTATTTGGAAATTTAACGAAGAGAAAGAAAGTCGGCAAAGGTGGAACACAATGGATGCAGTCAACGCTTTTAACCACGAGCTATTCTCCCTGATGGACTCAAAACCTCCAATCTCCAGGGCTAAGATGATCTCCATTACAAAATCTGCAATAAAAGCCATTAAATTATACAAACATGTTGTCCAGATTGTTGAGAAATTTATCAAAAAGTGCAAGCCTGAGTATAAAGTACCAGGACTCTATGTTGTGGACTCCATCGTGCGACAGTCGCGTCATCAGTTTGGTGCAGACAAGGATGTGTTTGGTCCCCGGTTCACTAAGAACATCACTGGGActtttgagaacctgtgcttatGTCCCACAGAGGACAGGAGTAAGATTGTGCGCGTCTTGAACCTGTGGCAAAAGAACGGCGTGTTTAAGATTGAGGTGATCCAGCCTCTCCTGGACATGGCTGCCGGATCCAGCAGCTCAGGCCCAGTTCCAGGTGTGGACAATGGCCCAGCTGCATCTCCTCCCTCCCCAGCAAGGGAAGCTGAGAGCCACACAGCAGTGTCGGTTAACTCCTGCAGCGCCGTGCCACAGCTGCAGAACTCGGACGCCTTTGCTGCTGTAGCTCAGCTCTTCCAGTCCTCGCAAGGCCAACAGCTCCAGCAGATGCTCCAGACGTTCCAGCAGCCCGGGAAGCCCCAGTCTCCAGCGCTGGAGAATAACATGATGACCCATCTCCAGATACAAGCCTCAGCTATTCAGCCCCCCACGGGTTTGGCACAGGGccacccacacaccacacagcctGCAGAGAAGAAAGCCACATTCGACAAGaaactTCTTGATCGTTTTGATTATGATGATGAAccagaaggaggagaagagacCAAGAGGGATGAGGCATCCTCTGTCCAGCCTGCCTTTGGCTTTGGAGAAGGTGTCCAGCCGCCTCAGCAGGCTTCAGCAGTCTTCTCTCAAGCTCCCAGTCAGATGCAACACTTTCAGCAACACATGATGGGCCTGAGTCAAGAACACCAGGTTCCATCTCCAAATGGACAGTCTCAGGCTTTCAACCGATTGCCACCTCAATCCTACCCAGGGATGATGCCACCAGGTGTAGGTCCCGCTGGTTTCCCCGGACCCTTCCCCCCTCAAAACAATGCCTTTCCTCAGCTCATGGCTGGACAGCAGCATCAGGAGGCCTCTGGGGAGATGGACACAAGACAGCACCAAGATGGCAGGAGGACACGGTCTAGGTCTGGTTCAAGATCTCCTAAAAGGAGGCGGTCACGGTCAGGTTCCCGTTCCAGACGTTTTCGACATCGACGGTCACGGTCTCGATCCAGAGAAAGGCGGCGCCACTCACCCCGCTCTCGCTCTCAGGAGAGGAGGGAACGGGAGAGGGAGCGAGAACGTAGACAGAAAGGCCTGCCTCCCATCAAACCTGACACTTTAAGTGTGTGCAGCACCACACTTTGGGTTGGCCAGCTGGACAAAAGGACACAACAGCAGGATGTGGCATGTCTATTAGAGGAGTTTGGCCAGATAGAGTCCATAAACATGATTCCTCCTCGAGGTTGTGCATACATTGTCATGGTTCATCGTCAGGATGCTTTTCGGGCTCTCCAGAAACTTAGCAGAGGCACTTACAAAGTCAACCAAAAAGCCATAAAGATTGCCTGGGCTCTAAACAAAGGGATTAAGTCAGAGTTCAAGCAGTATTGGGACGTAGAGCTTGGTGTCACCTATGTCCCCTGGTCCAAAGTCAAAATGGAAGATCTGGACGTTTTTAGAGAGGGGGGCATGCTGGATACAGATACACTCTCCCCAGAGTGGAAAGGGGTGCAGAGTGAACTGGAGACTGCGGACGACGCGCCTCAAAACGGCAGAAGTGACGTGGGCCAGATGGACGAGAGCCCGGCACTGCTCCCTGTGCAGGCTACTCCTGTCCAGCCAGTAGGGCCTTCTGGGCCAGTTGGGGTTCCACCCCCAGGTTTTCCTGCTGCCATGAATATCCCACCACCATCATTTCCACCAGGCGTTCCTCCTCCACCTGGACCTTTTATGAGGCCTGGGTTTAACCCCATGCAGATTCCTCCTGGATTTCTACCTCCGGGTGGCATGCCTCCTATTGGCACTGGGGGGCCTCCTCTTCCCACAGCGGGCATTGGCATGCCACCAGtTGGCAGCTCAGTTGAGGATTTGTCTGGTGATCCAGTAGGAATGGGCTCCAGGATCAATAGGGAAGGTGTAGACGGTTTCAATACTGGTCCAGGTAACCCGGTTCCACCAGGACCTCCACCTGGGATGAACATGCAAAATCCACCAGGGCTTTTAGGTACAAGACCAGGGGCGATGCCACTTCCGCCCCCAGGAATGCCCCCACCACCTCACCTGCAGCGCTTCCCGATGCCCCCCCCACGGCCCGGCATGCCCCCCATGCCCCCCCAGATGATGCCCCCCAGGGGCATGCCACAGATGATGCACCGTGAGCCTCCACCAGGGAGTTTTGGCAtgcctcctcctccatcacacGCCATCCGAGGCCCTTTTCCCCCTCCAGGCCCTCCATTCAGGGGAGAGCGGAATAGAGAGCAGGAGCGCTATGGAGGGCGCAGGCAGTTTGGGGGTGAACGGTCAGAAGGACGTGAGCGCTTTGGTGGATGGCATGAAGATCCGGAGTCAAGGGGAGGCTGGGACAGAGCGGGGTCGCGTAGAGACTGGAGGAGGAGtcctgatggagagagagaaagggagagggagcaagggagagaggaagaacGGGGCAAacgcagagacagagagagaagcacCCGCTGGGACAGGGACGACAGACTTGACAAACTTGAGCCTAATGGACACGAGATGCTCAGAGACTCGAGCAGCCGTGAGCGCCATAGTGATTCTACAAACGAAATGCCTCATGCCAAGGCAGAAGCTCCAGCTCCTTCCAAAGAAGGGAGTGCAGAGGTGGAAAATCAGAGCCAACCTGCAGAACAAACGAAGGCAGATCAATCCTAGGTCACACTAGGCTGTGGACTGGAactcttaagaaaaaaaaaaaaaaaaaaaaaaaaaatgtgtcctttttttttttttatcctaatcAGAAGCGTGTATCTGTGTGATCTTTTGCTAAAAACTATAGGAATACAGTCTAGAGTGGGACCGATATGATCACATTGCATGGGCTTAGATGTGATGGAAACGATCCCATAtgtaaagaggaaaaaaaaaacacatatcaTTCTTACTGTTAAGGCCAGGCCAGTGCCCTGTGTGCACTGATTTAAAATAAGCTTACTCCATGTCCATACCCATGCAGATTTTGGGCACTACATGCTAATGTGCAGAAATGATTCAGAAACATGCTTCATTCTTAAGCTCTGAGGTTTAATTCTAATTTTAATGCCTGGTCTTCCTCCAATGATTTCATTGACTTACAACGCAATTGACGTCAAGTGTCTGGCTAACATGGAGCACCGTCCTGTGAATCAGTGTCCATTATTGAGTTTAAATGTTGTACTAAGCCAGTGTTTCATATCCCTGTACTGCACATTTTGGTGGTTTTCCTGCTTTAACATGCCCatgtaaaaaaatcatgaagGGCTTCTTAATAGTTAATGAATTGAGTCAGGCATGTTGGGACTAGGGGCCAAGCTAGAATGGACAGTGCAGGACTATCCCATGAGTAagattggagaaaaaaaactgttttttaaacaaaaagacatggaaaaaatggaaaataactCTGCTGTAAATATGCTTAcatctaataatatttgtaGAGTTGGAAGTTTTTCTGAAGTATACTTCTGTCAGTGTCACCAATGGATCCTTGACTAAAATAAGAGACAAAGCCCCGTttgctgtaatgtttttaacctaCAGTGTTTACATTGTACCAGAGATGAGAtgtttgtataatttttaaGTTTGTGCAGATGTGAACTCATTTAATATTTCAGCAATGGGGATTCAGTTTTAATAAACTATTTTCATACCAAAATGAAAAAA

Function

symbol description
scaf4 Enables RNA binding activity and RNA polymerase II C-terminal domain phosphoserine binding activity. Involved in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled. Located in nucleoplasm.

NR:

description
PREDICTED: splicing factor, arginine/serine-rich 15 isoform X1

GO: NA

KEGG:

id description
K13167 SCAF4, SFRS15; SR-related and CTD-associated factor 4

RNA

RNA id representative length rna type GC content exon number start site end site
TU316348 False 1159 lncRNA 0.35 1 10881107 10882265
TU316349 False 950 lncRNA 0.37 1 10881107 10882056
XM_026941952.2 True 4132 mRNA 0.50 22 10865612 10882024

Neighbor

gene id symbol gene type direction distance location
postna postn coding upstream 53848 10776302 ~ 10811764 (+)
trpc4a trpc4,LOC108423767 coding upstream 105896 10738302 ~ 10759716 (+)
trim3b trim3b,LOC108276924,LOC108423836,LOC107701140,LOC107557229,LOC107720632,LOC107718737 coding upstream 311361 10520018 ~ 10554251 (+)
fhdc3 LOC108276923 coding upstream 346396 10507226 ~ 10519216 (+)
arfip2b arfip2b,LOC108276920,LOC108438961,LOC107718740,LOC107555180,LOC107701145,LOC107557232 coding upstream 360170 10485024 ~ 10505442 (+)
sod1 sod1 coding downstream 2011 10884276 ~ 10890564 (+)
tiam1a tiam1,LOC108423828 coding downstream 32437 10914702 ~ 10975096 (+)
grik1a grik1,grik1a,LOC107555187,LOC107701130,LOC107718733,LOC107693913 coding downstream 95829 10978094 ~ 11035327 (+)
cct8 cct8,LOC107693911 coding downstream 192390 11074655 ~ 11083609 (+)
tmem135 tmem135,LOC107701128,LOC107718730,LOC107693910,LOC107720646 coding downstream 201764 11084029 ~ 11098340 (+)
G266946 NA non-coding upstream 45873 10819526 ~ 10819739 (+)
G266901 NA non-coding upstream 130982 10732537 ~ 10734630 (+)
G266892 NA non-coding upstream 197298 10666818 ~ 10668314 (+)
G266871 frem2a,LOC108276566,LOC107701139,LOC107555183,LOC107693873,LOC107718779,LOC107720635 non-coding upstream 284430 10580859 ~ 10581182 (+)
G266869 NA non-coding upstream 293465 10571891 ~ 10572147 (+)
G267051 NA non-coding downstream 153733 11035998 ~ 11036230 (+)
G267062 NA non-coding downstream 159952 11042217 ~ 11042390 (+)
G267070 NA non-coding downstream 174347 11056612 ~ 11057021 (+)
G267090 NA non-coding downstream 203983 11086248 ~ 11087863 (+)
G267103 NA non-coding downstream 229121 11111386 ~ 11111597 (+)
G266868 LOC108276566 other upstream 294907 10569028 ~ 10570705 (+)
dclk1a dclk1,LOC107728871,LOC107577778 other upstream 1102915 9704360 ~ 9762697 (+)
LOC113543674 NA other upstream 1440757 9419665 ~ 9424855 (+)
G266161 NA other upstream 1529322 9335801 ~ 9336290 (+)
LOC113534874 LOC108276751 other upstream 1601501 9256943 ~ 9264111 (+)
vps36 vps36,LOC107701118 other downstream 3880048 14762313 ~ 14771073 (+)
trnar-ccu_11 NA other downstream 6205403 17087668 ~ 17087740 (+)
trnam-cau_40 NA other downstream 6205483 17087748 ~ 17087819 (+)
trnar-ccu_12 NA other downstream 6206184 17088449 ~ 17088521 (+)
trnam-cau_41 NA other downstream 6206264 17088529 ~ 17088600 (+)

Expression


Co-expression Network