G253444 (ssr4,LOC108275956,LOC108436301,LOC107671948,LOC107737640,LOC107741342,LOC107562474)


Basic Information

Item Value
gene id G253444
gene name ssr4,LOC108275956,LOC108436301,LOC107671948,LOC107737640,LOC107741342,LOC107562474
gene type non-coding
species striped catfish (Pangasianodon hypophthalmus)
category of species economic fish

Chromosome Information

Item Value
chromosome id NC_047610.1
NCBI id CM018556.1
chromosome length 25111544
location 11530704 ~ 11533297 (-)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome

Sequence

>TU300066
CTAGCTTTAACTTTCTGGTCGTgtgttggcaaaaaaaaaaaatctgacactgttacaaatgtttatttttattcaatgaATTTCATTGACAAGCAGACATTCCAAAAGCCAGAATGTGTCCTCTGTACATCAAGTCCACATCTAATAACACAGGTTATTACTCAGGCTTCTCCCAACTGCATCATAAAACAATCTCCTGGCTGGAACAAATTACTTACAAAACTGAGACATGAGCACTTGCTGGTACAAGAAATACATGTTTACATGACCGAGTTGCTTTTTCACACTTTTAGCACTTGACATATTTATGCCTGAATTGAACTTTTAGTGCTGTATGCCAGATAGTACAGAACAATGCCGATGACAGCTGCTAAGACCTCCGAGGACACCCAAGGACCACTCCATGCACCCCTGTGCTCTACATTGACAGAAAACAGAGGCTTGATGGCTTCTACATCTTCATTATTTCTCTGGGCCTTACGCAGGACGCTGTACGCCTCCTCATCAAAGAACTTCACTTGATAAGTGCCTGAGCTGGCTTGTTTGTGGGGAACACTCCAGGAAACCTGATTTTCCAACATCCTGACCTCTGGTCACAGGAAACTGTTTGCCATTAACATCTGCGTACAGGGCAACACTCtagtagagagagacagacacagagagatagagagagacaga
>TU300067
CTAGCTTTAACTTTCTGGTCGTgtgttggcaaaaaaaaaaaatctgacactgttacaaatgtttatttttattcaatgaATTTCATTGACAAGCAGACATTCCAAAAGCCAGAATGTGTCCTCTGTACATCAAGTCCACATCTAATAACACAGGTTATTACTCAGGCTTCTCCCAACTGCATCATAAAACAATCTCCTGGCTGGAACAAATTACTTACAAAACTGAGACATGAGCACTTGCTGGTACAAGAAATACATGTTTACATGACCGAGTTGCTTTTTCACACTTTTAGCACTTGACATATTTATGCCTGAATTGAACTTTTAGTGCTGTATGCCAGATAGTACAGAACAATGCCGATGACAGCTGCTAAGACCTCCGAGGACACCCAAGGACCACTCCATGCACCCCTGTGCTCTACATTGACAGAAAACAGAGGCTTGATGGCTTCTACATCTTCATTATTTCTCTGGGCCTTACGCAGGACGCTGTACGCCTCCTCATCAAAGAACTTCACTTGATAAGTGCCTGAGCTGGCTTGTTTGTGGGGAACACTCCAGGAAACCTGATATTTTCCAACATCCTGACCTCTGGTCACAGGAAACTGTTTGCCATTAACATCTGCGTACAGGGCAACACTCTGTGCTCCATTTCCACATGCCAGACTCAGCTCAACAATGAAGACTGTCTCGGAGGAGATCACTGCATCAGCTGTTGTGTATGAAGAGGTGGAGATCACCGGCTCTGTGCAAGTGTCAGCTGGGAGGagagaaacactttttttttacaaacatgaTTGATTTATCCAAGCCATAGAAGATCCCAGATTTAGTAATCCTAGCATTTCCCTAATCTCATTATCTAGGCTGTTTGATCAAAGTTCAGAGACTGTAGCTTACAACTATTTAGAGCTATTTGGATGTTAAATGAactttacagtacagtacagtacagtagagaCAGCTAATAATCACAAACACTTATAACATATGATCAGCTTTAACAGTTATGCTCCTGGCTGGTTTAAAAGTCGACCTAAATAACGCACTAAcatcacaaatacaaaaatgaccAACATAAAAATCTTCACCTGCACACAGAGTCAGACAAAAAGCCACAAGAGCTACAATTATTCTCCTCATTTTGCTTCTTGGCTGGTCGCGAGAACTCAAAGGAAGC

Function

symbol description
ssr4 Acts upstream of or within cellular response to estrogen stimulus. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be integral component of membrane. Predicted to be active in endomembrane system. Is expressed in several structures, including axis; endocrine system; hatching gland; notochord; and polster. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation Iy. Orthologous to human SSR4 (signal sequence receptor subunit 4).

GO: NA

KEGG: NA

RNA

RNA id representative length rna type GC content exon number start site end site
TU300066 False 681 lncRNA 0.42 4 11532274 11533297
TU300067 True 1180 lncRNA 0.41 5 11530704 11533297

Neighbor

gene id symbol gene type direction distance location
emp3b LOC108275556,LOC107562456,LOC107671979,LOC107737636,LOC107741326,LOC107560919,LOC108436335,LOC107657024,LOC105894294 coding downstream 86449 11438049 ~ 11444255 (-)
LOC113530844 LOC108275904,LOC108436332 coding downstream 154144 11372242 ~ 11376560 (-)
fkbpl fkbpl coding downstream 253028 11274090 ~ 11277676 (-)
trnan-guu_24 NA coding downstream 257301 11273330 ~ 11273403 (-)
trnae-uuc_4 NA coding downstream 271590 11259043 ~ 11259114 (-)
LOC113530846 idh3g,LOC108275983,LOC108436344,LOC108425561 coding upstream 54408 11587705 ~ 11598386 (-)
LOC113530831 LOC108275674,LOC108436304,LOC107657035,LOC107741317,LOC105906744,LOC107560879 coding upstream 184532 11717829 ~ 11725337 (-)
uba3 uba3,LOC108435248 coding upstream 195704 11729001 ~ 11741759 (-)
LOC113530815 LOC108276064,LOC108276065,LOC108276066,LOC108275619 coding upstream 288551 11821848 ~ 11850443 (-)
LOC113530817 LOC108276066,LOC108276064,LOC108276065,LOC108275619 coding upstream 295978 11829275 ~ 11834195 (-)
G253384 NA non-coding downstream 166290 11362972 ~ 11364414 (-)
G253385 NA non-coding downstream 169119 11359515 ~ 11361585 (-)
G253383 NA non-coding downstream 176487 11353502 ~ 11354217 (-)
G253174 NA non-coding downstream 265555 11264909 ~ 11265149 (-)
LOC113530615 fam208a non-coding downstream 439369 11089065 ~ 11091335 (-)
G253430 LOC108275954 non-coding upstream 6884 11540181 ~ 11542479 (-)
G253463 NA non-coding upstream 38128 11571425 ~ 11571624 (-)
G253464 NA non-coding upstream 38523 11571820 ~ 11572019 (-)
G253433 NA non-coding upstream 79943 11613240 ~ 11620395 (-)
G253494 NA non-coding upstream 179700 11712997 ~ 11714753 (-)
LOC113530309 NA other downstream 67998 11456020 ~ 11462706 (-)
abhd6b LOC108275644,LOC108436291 other downstream 505695 11020531 ~ 11025009 (-)
LOC113530950 smim4,zgc:193598,LOC108436318,LOC108276132,LOC107570281 other downstream 515038 11009463 ~ 11015666 (-)
sinup NA other downstream 891986 10636501 ~ 10638718 (-)
usp21 LOC108276040,LOC108432659 other downstream 1060908 10460694 ~ 10469796 (-)
avpr2ab avpr2,avpr2ab,LOC108275514,LOC106567019,LOC106572707,LOC108436342,LOC107672000 other upstream 16097 11549394 ~ 11568603 (-)
LOC113530816 LOC108276066,LOC108276064,LOC108276065,LOC108275619 other upstream 305499 11838796 ~ 11859346 (-)
ptk6b LOC108276246 other upstream 622431 12155728 ~ 12167795 (-)
plagl2 plagl2,LOC107690855,LOC107681868,LOC107559482,LOC107747490,LOC107558237,LOC107707758 other upstream 1364177 12897474 ~ 12934308 (-)
oprl1 oprl1,LOC107681404,LOC107727003,LOC107666560 other upstream 1717843 13251140 ~ 13283885 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000001_05295894_05308912 SSR4, SSRD, IKBKG coding CI01000001 null 5295523 ~ 5308986 (-)