RNA id: TCONS_00049500


Basic Information

Item Value
RNA id TCONS_00049500
length 3205
RNA type mRNA
GC content 0.49
exon number 4
gene id XLOC_024953
representative True

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 1492174 ~ 1501255 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

TTTTTTCTCGCTCTTCACACAACGGGGCTCTTTAAGCCTCGACGCGCGACACAGAGCAGGCATTCAGAGCGCGAGCGAGGGGGCTGAACCGACGGACTCTCGCGCTGGGCGGGCGACCTGCTGCACTGTAAAgTTTCCATCAGATCTATATTCAGAGGAAGACGGCGGAAGGATTCCTTCTTACAATCTCGAATTATATAAAAAGAACTGTTAAGGTTTCACTGGATGatcttaaataataaacaaaagcacagttgttttacaagaaaaaacatttgtaaagtataaataaatacatttatatttaagatAAAATTTAAGTGAGGAAATTAGACCTACCGAAGTCACCTGTGGCCGCAGAACGAGTGGACCGATGTCGGCGGAGGAGCACAGCATGTCGGAGGTGGAAATGAGTCCCGGGGTGTCGGACGATGGGCACTCCATGTCCCCTGGTCACTCGTCGGGCGCTCCAGGTGGCGCGGACTCCCCTCTGCCCGGTCAGCAGTCTCAGATGTCCGGGATCGGGGATGATGGAGCCGGTGTCTCCGGCGGGGTCTCAGTGAAGTCCGACGAGGAAGATGACCGGTTCCCCATCGGCATCCGCGAGGCGGTCAGTCAGGTGCTGAACGGGTACGACTGGACGCTCGTGCCCATGCCCGTGCGCGTGAACTCGGGCAGCAAGAGCAAACCGCACGTCAAGCGGCCGATGAACGCGTTCATGGTGTGGGCGCAGGCCGCGCGCAGGAAACTGGCGGATCAATATCCGCACCTGCACAACGCCGAGCTCAGCAAAACACTGGGGAAGCTGTGGAGACTGCTGAACGAGACGGATAAGCGGCCGTTTATCGAGGAGGCCGAGCGCTTGAGGAAGCAGCATAAGAAAGATTATCCCGAGTACAAGTACCAGCCACGTCGACGCAAGAACGGCAAACCGGGTTCCAGCTCAGAGGCCGACGCCCACTCTGAGGGTGAGGTCAGCCACAGCCAATCGCATTACAAGAGCCTGCACCTGGAGGTGGCGCACGGCGGGGCTGCAGGGTCACCATTGGGTGATGGACACCACCCTCACGCTACAGGTCAGAGTCACAGCCCTCCAACGCCCCCTACCACCCCCAAGACGGAACTGCAGGGAGGAAAATCAGGCGAGGGCAAGCGTGAGGGCGGAGCCTCTCGGAGTGGACTGGGGGTGGGAGCAGATGGAAGCTCCGCCTCATCGTCTGCCAGCGGGAAACCGCACATCGACTTCGGTAACGTGGACATTGGCGAAATCAGCCATGACGTGATGGCCAACATGGAGCCGTTCGACGTGAACGAGTTCGACCAGTATCTCCCACCCAATGGCCACCCGCAGGCGTCCGCCACTGCCAGCGCAGGATCTGCAGCGCCATCGTATACATACGGCATCTCCAGCGCGCTAGCGGCCGCTAGTGGCCACTCCACCGCATGGCTGTCCAAGCAGCAACTGCCGTCCCAGCAGCATTTGGGCGCAGATGGCGGGAAAACGCAGATAAAGAGTGAAACACACTTCCCTGGGGATACAGCGGCGAGCGGTTCACACGTCACATACACGCCGCTAACACTGCCGCACTACAGCTCCGCCTTCCCCTCGCTGGCGTCCCGCGCACAATTCGCCGAATACGCCGAGCACCAGGCCTCGGGATCCTACTACGCCCACTCCAGCCAGACCTCAGGCCTCTACTCCGCCTTCTCCTACATGGGCCCCTCACAGCGGCCCCTGTACACCGCCATTCCGGATCCGGGATCCGTGCCGCAGTCACACAGCCCTACGCATTGGGAGCAGCCCGTATACACCACACTGTCTCGACCGTGACACACTCTACCAAGATGACCAGTCACTAAAGGTCCAACcgtaaggtgtgtgtgtgtgtgtgctaaaaaTCATCGAAACACTCGCCTGCACCACAATCGACACAAACTGAGATCTGagaaaagagtgtgtgtgtgtgtggagatctGCAGGGAAATATTCTCACGTGCCTCAGACGACCACCGTCCAGACCTGCTCCCTCAACGCCAATTTGAACACCAGTAGTATTTTCGAAAAAGACGTATTACCAAAGTACCGAGACCAAAACATTACAGAAATACGAGAGTGCATCCATCCTTCCTGAACTCCGGATATCAGATCACACACAGACTTCAACACATGATGCTAGTACCTGTGCATCCGCATTTTTTTATCTGTATttgtatgaatgaataatcttTTTATTAACCAAAATAAGgccatattgtttttaaaaaaataatgaggtGTTTTTCGTTGTTGTAATCTCTTGTGTTGTCGTTACTGTTGTTATTTGTGTTGCCATAACTACACTGAAAAGTCTTCACCACTGTCTAGTGTTTGTTAatgacatttgtgttttatgaCTTTCAGCGTGTGTAAATATCAGTGCCAGGACGCCATACACACATGTCTCCACCCAATTAAGGTGCGCTCACAGTGACGTTAGTTAAATTGAGGAATTCCCAACCATGCAAATTCCTCTAGAAATGGCTATATTTCGTGAAAGCAGTAAATGTGAGCGCACCTTTATTTCACACAAGCAGTACTGTAAAGGTAATATATTTTTGCCAGATTGGAAATAGTGGACGTAATTAcgaatttttaataataaatgactatttttagAGAATACCGCTAGTGCCTCAAGTCCATCACAAACGAATTGTCGTTTCTGATAAATTCAATTTTGATGATGTAAAATCCTTTTCAGGGTGCAAATTTTATCATGCGTTAACCGATGTGATTATACATCGAATATGCATATGCAAATTAATAAGTgccatttttataattaaaaatacatcaaCTATCTGAAGACCTTCCTAACATtgggtaagtaaataaatacatttatttcattgTATTATTTTTGGTAAATACAATATTTAGCTATTCTATGTTTTGTCTCCCTTTGGTactttatagttttgtttttgccctctttattatttagtattattcagaaacaaacaaactctttttatatattacagaatattatttatatttgttgttgttttttttatcagtagCGTTTTATTCTGTTTGTCGTAAACCTCTGTCGTGTGCTGTTGTGGTGGGTTAAAGTGCTGTTGTTTTTCTCTGTCGGTGTAAATAGAACTGAGAGCAGTGACTAACTTTCCTCACTCTAAATAAAGCTGCAGTCTTTACGAA

Function

GO:

id name namespace
GO:0021782 glial cell development biological_process
GO:0048752 semicircular canal morphogenesis biological_process
GO:0010628 positive regulation of gene expression biological_process
GO:0048484 enteric nervous system development biological_process
GO:0002009 morphogenesis of an epithelium biological_process
GO:0001755 neural crest cell migration biological_process
GO:0071600 otic vesicle morphogenesis biological_process
GO:0050931 pigment cell differentiation biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0048839 inner ear development biological_process
GO:0048840 otolith development biological_process
GO:0014032 neural crest cell development biological_process
GO:0050768 negative regulation of neurogenesis biological_process
GO:0014037 Schwann cell differentiation biological_process
GO:1904888 cranial skeletal system development biological_process
GO:0014044 Schwann cell development biological_process
GO:0043473 pigmentation biological_process
GO:0010001 glial cell differentiation biological_process
GO:0048066 developmental pigmentation biological_process
GO:0030318 melanocyte differentiation biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0007422 peripheral nervous system development biological_process
GO:0022011 myelination in peripheral nervous system biological_process
GO:0060041 retina development in camera-type eye biological_process
GO:0048709 oligodendrocyte differentiation biological_process
GO:0021772 olfactory bulb development biological_process
GO:0005634 nucleus cellular_component
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function
GO:0003677 DNA binding molecular_function
GO:0000987 cis-regulatory region sequence-specific DNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-011207-1 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in olfactory bulb development. Acts upstream of or within with a positive effect on iridophore differentiation; melanocyte differentiation; and xanthophore differentiation. Acts upstream of or within several processes, including nervous system development; neural crest cell migration; and sensory organ development. Predicted to be active in nucleus. Is expressed in several structures, including glioblast; head; iridoblast; nervous system; and neural crest. Used to study Hirschsprung's disease and Waardenburg's syndrome. Human ortholog(s) of this gene implicated in Kallmann syndrome; PCWH syndrome; Waardenburg syndrome type 2E; and Waardenburg syndrome type 4C. Orthologous to human SOX10 (SRY-box transcription factor 10).

Ensembl:

ensembl_id ENSDART00000112979

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00049499 lncRNA upstream 223349 1260360 ~ 1268825 (+) True XLOC_024952
TCONS_00052526 lncRNA upstream 255457 1235024 ~ 1236717 (+) False XLOC_024951
TCONS_00052527 lncRNA upstream 255457 1235405 ~ 1236717 (+) True XLOC_024951
TCONS_00049493 lncRNA upstream 300832 1187244 ~ 1191342 (+) True XLOC_024947
TCONS_00049488 lncRNA upstream 338125 1150386 ~ 1154049 (+) True XLOC_024944
TCONS_00052303 lncRNA downstream 53644 1554899 ~ 1563730 (+) False XLOC_024954
TCONS_00052528 lncRNA downstream 71595 1572850 ~ 1577061 (+) False XLOC_024955
TCONS_00052529 lncRNA downstream 75498 1576753 ~ 1597978 (+) False XLOC_024955
TCONS_00049507 lncRNA downstream 88309 1589564 ~ 1590504 (+) False XLOC_024956
TCONS_00049506 lncRNA downstream 88309 1589564 ~ 1590504 (+) True XLOC_024956
TCONS_00049498 mRNA upstream 264044 1223824 ~ 1228130 (+) True XLOC_024950
TCONS_00049497 mRNA upstream 269925 1219344 ~ 1222249 (+) True XLOC_024949
TCONS_00049496 mRNA upstream 273947 1211280 ~ 1218227 (+) True XLOC_024948
TCONS_00049495 mRNA upstream 273996 1211242 ~ 1218178 (+) False XLOC_024948
TCONS_00049494 mRNA upstream 274006 1209006 ~ 1218168 (+) False XLOC_024948
TCONS_00049508 mRNA downstream 136103 1637358 ~ 1639983 (+) True XLOC_024959
TCONS_00049509 mRNA downstream 187965 1689220 ~ 1704409 (+) False XLOC_024960
TCONS_00049510 mRNA downstream 197175 1698430 ~ 1714615 (+) True XLOC_024960
TCONS_00049511 mRNA downstream 223686 1724941 ~ 1729813 (+) True XLOC_024961
TCONS_00049512 mRNA downstream 233959 1735214 ~ 1737590 (+) True XLOC_024962
TCONS_00049471 other upstream 637544 842733 ~ 854630 (+) True XLOC_024931
TCONS_00049457 other upstream 1069436 420342 ~ 422738 (+) True XLOC_024918
TCONS_00049501 other downstream 53047 1554302 ~ 1559477 (+) False XLOC_024954
TCONS_00049502 other downstream 55598 1556853 ~ 1682090 (+) True XLOC_024954
TCONS_00049503 other downstream 71595 1572850 ~ 1576295 (+) False XLOC_024955
TCONS_00049504 other downstream 75498 1576753 ~ 1586425 (+) False XLOC_024955
TCONS_00049505 other downstream 84799 1586054 ~ 1588601 (+) True XLOC_024955

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01054460_00015714_00018657.mRNA True 3002 mRNA 0.51 3 CI01054460 15420 ~ 19901 (-)
striped catfish (Pangasianodon hypophthalmus) TU93651 True 1562 lncRNA 0.36 3 NC_047599.1 8251437 ~ 8254209 (+)
bowfin (Amia calva) TU93651 True 1549 TUCP 0.56 4 CM030128.1 41393504 ~ 41405025 (+)