XLOC_003382 (rpusd4)


Basic Information

Item Value
gene id XLOC_003382
gene name rpusd4
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 17964689 ~ 18081864 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00006630
AGCTGCGGATGAGTTTCCCGGTAAAGAGCTTTCCAGGAATGCTGAAACAGTGGCTGAAATTGACCTCTGCGCCTCTTGCTGCAGCATTGCACTGAGAGATCCCTGATGATGGTGATTATGCATGGGGTGGTGTGACTGCAAGggtagccacagcggaatgaaccgccaacttatccagcatatctttaaagcagcggatgcccttccagacgcaacccatcactgggaaacgtccatacgcactcatacactacggacaatttagcctgcatgtctttggacttgtgggggaaactgcatgcaaacacagggaaaacatgcaaactccacacagaaacgtcaactgacccagccgagactcgaaccagcgactttcttgctgtgctGTGAactcgctacccactgcgccaccgtgcagcctctGCAGtggTTTCAGACACCCAGACCGTCGCTTCAAAACACAAAACAGCACCGAAAGCAGCAGACATCGCCAACAGACTccggaaagagaaagagaaagaaaaagatgaCAAAAACGAGGTTCCGGTGTCCCCTCTCCAGTCCAGAGTGAATGAACTCAAGCAGTTTTCTCAGCAGCTGCAGTCTGTGCACCCGAGTGTGTTCGCAAAAGCCCTTTACAGGAGCTCCCTTTATGAAGACCAAAACATAATCGCCATAAATAAACCATATGACGTTCCTTTGCATA
>TCONS_00006631
gtgacttttattttgaactgTAGTTAAGTCATGCTGCCGCTATGCTGTAGGTAGTTTACCCTTGATTATTTGACTTTATCAgtaatttttgtattatatttattacatatcTGCCTGTGAGAAATTCAAGATCTCGGAGCATTGGTCGTTGGAAACAGAATTTAACTGAACCATTCATTTTGTGAAAATGCGACACGCACGTGAGGTGACATTTGCGAGACTCATGAGGACATTTGCCGCAGTTTCAGACACCCAGACCGTCGCTTCAAAACACAAAACAGCACCGAAAGCAGCAGACATCGCCAACAGACTccggaaagagaaagagaaagaaaaagatgaCAAAAACGAGGTTCCGGTGTCCCCTCTCCAGTCCAGAGTGAATGAACTCAAGCAGTTTTCTCAGCAGCTGCAGTCTGTGCACCCGAGTGTGTTCGCAAAAGCCCTTTACAGGAGCTCCCTTTATGAAGACCAAAACATAATCGCCATAAATAAACCATATGACGTTCCTTTGCATAATATAAATGGCATCAGAAACAGTATCGCCGAGTGTCTGCCTTTGCTGGCAAAGATCACGGATAATATGCGACCTGGATCACAGTTACATCTTTGCCACAAACTGGAAAAAGAAACTACTGGAGTTTTGATCCTGGCTAAAACAGAGGAAGCTGCTGAACATGTCCAAACGCTCATCCAATCACACAAAGTGGAAATGAAATACTTGGCAATCACTGTAGGTGTGCCTGTTCCATCTGAAGGAGTGATAGACATTCCTGTTATAGAGAGAGCAGTTGTGGGACCTCAGCCGCACTTTAAGATGGCTCTGAGTCCGCTGTTTAAAGTGAATGAGGATGGAGATGGAGTGACGAGAGTGCGAGCTCACAGACAGGCACATGCTGCAGTCACACGGTATCAAGTTCTGGACAACACCAGCGGCTGCAGTTTAGTGGAACTCCAGCCTCTCACAGgtgtgaaAAACCAACTTCGAGTGCACATGGCTTTAGCGTTGACCTGCCCCATTCTTGGTGACCATAAATATTCCCACTGGAGCAAACTAGCACCCCAGAAGCTGCCTGAGGGTACGCTGCGCCGGCTGGGCCTGGTTCAGAGTAAAACACGATACCTGCCTCTTCATCTACACTCCCGAAGGATCGTCCTGCCAGGATTCAAAGGTCACAGAGACATTACGGTGTCCTGTCCCCTTCCCAAATACTTCATCAACGCATTGAAGAGGCTGGAGATCCCACTGCCGGCAAAAGAATGAGATCTATGATCTCTTCTTACTTTTGCATCGAGGACTGGATTTGACATGGTTGAAACTGGACCTTCTGCTCAGATGTTttgtatgaaataaataaaagaccAATAAAAATGTTCTGCAAACTAAAgatataatcaagtcttcattaGTTATCAgtgtcaaaaataaacaaacccaTATCCTTTAAGGTGAAATACTTGCATATAGATTTATATAAAGACAGTTTTTTATAATTAGACTTTAACTGATTACTTGACAAGCAATCAGAATAATTGGAAGTCACAAATGTAAAAATCTGTTGTTAATTAAAGGGTAGGGCTGCAGTATTATGATACTATGCTCTTGTGTAGACCATCATTTTATACTGTATTCATGCAAACAGGATGTTATGTCATGGCTCTACAGGCTGAACTTCATATCAGTCCATGACGATACAGTAGTGAATTATGCTAAAGATCAAATTAAATTCTGAAACGCCTTTGATTGA
>TCONS_00006632
tgacttttattttgaactgTAGTTAAGTCATGCTGCCGCTATGCTGTAGGTAGTTTACCCTTGATTATTTGACTTTATCAgtaatttttgtattatatttattacatatcTGCCTGTGAGAAATTCAAGATCTCGGAGCATTGGTCGTTGGAAACAGAATTTAACTGAACCATTCATTTTGTGAAAATGCGACACGCACGTGAGGTGACATTTGCGAGACTCATGAGGACATTTGCCGCAGTTTCAGACACCCAGACCGTCGCTTCAAAACACAAAACAGCACCGAAAGCAGCAGACATCGCCAACAGACTccggaaagagaaagagaaagaaaaagatgaCAAAAACGAGGTTCCGGTGTCCCCTCTCCAGTCCAGAGTGAATGAACTCAAGCAGTTTTCTCAGCAGCTGCAGTCTGTGCACCCGAGTGTGTTCGCAAAAGCCCTTTACAGGAGCTCCCTTTATGAAGACCAAAACATAATCGCCATAAATAAACCATATGACGTTCCTTTGCATAATATAAATGGCATCAGAAACAGTATCGCCGAGTGTCTGCCTTTGCTGGCAAAGATCACGGATAATATGCGACCTGGATCACAGTTACATCTTTGCCACAAACTGGAAAAAGAAACTACTGGAGTTTTGATCCTGGCTAAAACAGAGGAAGCTGCTGAACATGTCCAAACGCTCATCCAATCACACAAAGTGGAAATGAAATACTTGGCAATCACTGTAGGTGTGCCTGTTCCATCTGAAGGAGTGATAGACATTCCTGTTATAGAGAGAGCAGTTGTGGGACCTCAGCCGCACTTTAAGATGGCTCTGAGTCCGCTGTTTAAAGTGAATGAGGATGGAGATGGAGTGACGAGAGTGCGAGCTCACAGACAGGCACATGCTGCAGTCACACGGTATCAAGTTCTGGACAACACCAGCGGCTGCAGTTTAGTGGAACTCCAGCCTCTCACAGgtgtgaaAAACCAACTTCGAGTGCACATGGCTTTAGCGTTGACCTGCCCCATTCTTGGTGACCATAAATATTCCCACTGGAGCAAACTAGCACCCCAGAAGCTGCCTGAGGGTACGCTGCGCCGGCTGGGCCTGGTTCAGAGTAAAACACGATACCTGCCTCTTCATCTACACTCCCGAAGGATCGTCCTGCCAGGGTTCAAAGGTCACAGAGACATTACGGTGTCCTGTCCCCTTCCCAAATACTTCATCAACGCATTGAAGAGGCTGGAGATCCCACTGCCGGCAAAAGAATAAGATTTATGATCTCTTCTTACTTTTGCATCGAGGACTGGATTTGACATGGTTGAAAATGGACCTTCTGCTCGGATGTTttgtatgaaataaataaaagaccAATAAAAATGTTCTGCAAAC
>TCONS_00006633
ATGCGACACGCACGTGAGGTGACATTTGCGAGACTCATGAGGACATTTGCCGCAGTTTCAGACACCCAGACCGTCGCTTCAAAACACAAAACAGCACCGAAAGCAGCAGACATCGCCAACAGACTccggaaagagaaagagaaagaaaaagatgaCAAAAACGAGGTTCCGGTGTCCCCTCTCCAGTCCAGAGTGAATGAACTCAAGCAGTTTTCTCAGCAGCTGCAGTCTGTGCACCCGAGTGTGTTCGCAAAAGCCCTTTACAGGAGCTCCCTTTATGAAGACCAAAACATAATCGCCATAAATAAACCATATGACGTTCCTTTGCATAATATAAATGGCATCAGAAACAGTATCGCCGAGTGTCTGCCTTTGCTGGCAAAGATCACGGATAATATGCGACCTGGATCACAGTTACATCTTTGCCACAAACTGGAAAAAGAAACTACTGGAGTTTTGATCCTGGCTAAAACAGAGGAAGCTGCTGAACATGTCCAAACGCTCATCCAATCACACAAAGTGGAAATGAAATACTTGGCAATCACTGTAGGTGTGCCTGTTCCATCTGAAGGAGTGATAGACATTCCTGTTATAGAGAGAGCAGTTGTGGGACCTCAGCCGCACTTTAAGATGGCTCTGAGTCCGCTGTTTAAAGTGAATGAGGATGGAGATGGAGTGACGAGAGTGCGAGCTCACAGACAGGCACATGCTGCAGTCACACGGTATCAAGTTCTGGACAACACCAGCGGCTGCAGTTTAGTGGAACTCCAGCCTCTCACAGgtgtgaaAAACCAACTTCGAGTGCACATGGCTTTAGCGTTGACCTGCCCCATTCTTGGCGACCATAAATATTCCCACTGGAGCAAACTAGCACCCCAGAAGCTGCCTGAGGGTACGCTGCGCCGGCTGGGCCTGGTTCAGAGTAAAACACGATACCTGCCTCTTCATCTACACTCCCGAAGGATCGTCCTGCCAGGGTTCAAAGGTCACAGAGACATTACGGTGTCCTGTCCCCTTCCCAAATACTTCATCAACGCATTGAAGAGGCTGGAGATCCCACTGCCGGCAAAAGAATAA

Function

symbol description
rpusd4 Predicted to enable pseudouridine synthase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis. Predicted to act upstream of or within pseudouridine synthesis and tRNA processing. Predicted to be located in mitochondrial matrix. Orthologous to human RPUSD4 (RNA pseudouridine synthase D4).

GO:

id name namespace
GO:0001522 pseudouridine synthesis biological_process
GO:0000455 enzyme-directed rRNA pseudouridine synthesis biological_process
GO:0009451 RNA modification biological_process
GO:0008033 tRNA processing biological_process
GO:0005759 mitochondrial matrix cellular_component
GO:0005739 mitochondrion cellular_component
GO:0003723 RNA binding molecular_function
GO:0016853 isomerase activity molecular_function
GO:0009982 pseudouridine synthase activity molecular_function

KEGG:

id description
ko03016 Transfer RNA biogenesis
ko03029 Mitochondrial biogenesis

ZFIN:

id description
ZDB-GENE-040801-238 Predicted to enable pseudouridine synthase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis. Predicted to act upstream of or within pseudouridine synthesis and tRNA processing. Predicted to be located in mitochondrial matrix. Orthologous to human RPUSD4 (RNA pseudouridine synthase D4).

Ensembl:

ensembl_id ENSDARG00000012674

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00006630 False 706 processed_transcript 0.50 4 17964689 17984774
TCONS_00006631 False 1748 mRNA 0.42 7 17984167 17994777
TCONS_00006632 False 1383 mRNA 0.45 7 17984168 18081864
TCONS_00006633 True 1077 mRNA 0.49 7 17984354 18081744

Neighbor

gene id symbol gene type direction distance location
XLOC_003381 NA coding upstream 1236 17956841 ~ 17963453 (+)
XLOC_003380 NA coding upstream 12131 17951563 ~ 17952558 (+)
XLOC_003379 NA coding upstream 32531 17930273 ~ 17932158 (+)
XLOC_003378 CR589944.3 coding upstream 44676 17919143 ~ 17920013 (+)
XLOC_003377 BX571952.1 coding upstream 451057 17440591 ~ 17513632 (+)
XLOC_003386 zgc:175135 coding downstream 48436 18130300 ~ 18132066 (+)
XLOC_003387 zgc:173545 coding downstream 75396 18157260 ~ 18158883 (+)
XLOC_003388 zgc:173545 coding downstream 94029 18175893 ~ 18177499 (+)
XLOC_003389 LO018315.6 coding downstream 101356 18183220 ~ 18200701 (+)
XLOC_003390 tmcc1b coding downstream 123902 18205766 ~ 18244561 (+)
XLOC_003369 CR854846.2 misc upstream 1841607 16122786 ~ 16123082 (+)
XLOC_003318 CR450764.6 misc upstream 5252693 12711700 ~ 12711996 (+)
XLOC_003317 CR450764.16 misc upstream 5270426 12693967 ~ 12694263 (+)
XLOC_003316 CR450764.11 misc upstream 5279090 12685304 ~ 12685599 (+)
XLOC_003315 CR450764.18 misc upstream 5284661 12679732 ~ 12680028 (+)
XLOC_003392 BX296530.1 non-coding downstream 594578 18676442 ~ 18676557 (+)
XLOC_003393 NA non-coding downstream 620498 18702362 ~ 18708059 (+)
XLOC_003394 NA non-coding downstream 659163 18741027 ~ 18742103 (+)
XLOC_003395 CU207354.2 non-coding downstream 751049 18832913 ~ 18833246 (+)
XLOC_003402 BX276115.1 non-coding downstream 1951202 20033066 ~ 20033185 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000058_04758962_04763056 RPUSD4 coding CI01000058 null 4758962 ~ 4763056 (-)