XLOC_015417 (rnf2)


Basic Information

Item Value
gene id XLOC_015417
gene name rnf2
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007113.7
NCBI id CM002886.2
chromosome length 59640629
location 23351454 ~ 23361933 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00030857
AGAACGCGCTGGCAGGAGAGAGAGTGTTCACAACATTGAGATAAAAGACGTGGTGTATGAAGATGACACAGACGGTCCAGACAAATGGGGTTCAACCCCTCAGCAAGACCTGGGAGCTCAGTCTATATGAATTACAGAGAACTCCACAGGAGGCCATCACGGATGGTCTGGAGATTGCAGTGTCCCCACGCAGCCTGCACAGTGAGCTTATGTGTCCCATCTGCCTGGACATGCTGAAGAACACTATGACCACCAAGGAATGCCTGCACCGTTTCTGTGCCGACTGCATCATCACTGCTCTCAGATCAGGGAATAAGGAGTGTCCAACATGCAGAAAGAAGCTGGTGTCTAAGCGCTCTCTTCGTCCAGACCCTAACTTTGACGCTCTGATCAGTAAGATCTACCCCAGCAGAGACGAATACGAAGCCCACCAGGAGAGAGTGCTGGCCCGCATCAGCAAACACAACAACCAGCAGGCGCTCAGCCACAGTATCGAAGAAGGCCTAAAAATCCAGGCCATGAACAGACTGCAGCGGGGGAAGAAGCATCAAATTGAAAACGGCAGCGGGGCAGAGGACAATGGGGACAGTTCACATTGCAGCAATGCATCAGTGCACAGTAACCAAGAGGCTGGACCCAGCATCAAACGAACCAAAACCTCAGATGACTCTGGACTGGACATGGACAATGCCACTGAGAATGGAGGAGGAGACATTGCGCTGGATGGAGTCAGCGAGATTGAGCTCGTGTTTCGTCCTCACCCAACGCTGATGGAGAAAGAAGACGCCGCTCAGACAAGGTACATCAAGACTTCAGGGAACGCCACAGTGGACCACCTTTCCAAATACTTGGCTGTCAGATTGGCTCTGGAGGAAATGCGCAAGAATGGAGAGGCAAGCCCCATCAATGTAGAGGCCGCCAGTGAAAAACAGTACACAATCTACATCCCTACAGCAAGCAACCAGTTCACAGTCCTGAATGGCTCTTTCTCCCTGGAGCTGGTGAGCGAAAAGTACTGGAAGGTCAACAAGCCCATGGAGTTGTACTTCGCCCCAACGAAGGAACACAAATGAGCCCTGTGAGACACAAGGGTCTTAATTGACCCAGGACAGATTGAAGGTTCATCCTctcctctcttctctctctccctGTTCCTTTCTGTATTTTTCTCGCTGTTTCTCCTCATCTGGAGTTTACTAGTCTCTGGATCCCTCAATAACTGTGCTGCTttgatttggttttgttttttgtatggcTTTTTGTATGGGAATGAGACTAGGGTCCTTCATCGGGGTTGGAGGGACATTGAAGTTTTGGATTCATCCCCCCTCTTTAAGTTGACACAATCGTTATTACATGTGAAGTCCTTTTTGCATCAAGAGGACTGTGACGTTGCCTTCAACAAGCCAAAATATTAGTCTCCAATTGCAACCGTATCATCATGGGAAAGTCCTCTCGAGTGCTTCATGTAAGACTCTGTCAGAAAGTGGCTTTTGTAGCCAATGGCGCTGTCCATTATAATCCGACTTGACCAATGATTTGAGAGATTTCAAGTGCATTTTCTGACAACACCATTCCTGTAGCAGCAACATTTGTTCACAAATCTGACTGCATCTTGACACTGTGTACCAGTACATTGCGTTGGCTTGGGTCACATGACAGCGTCATGTCACTTGTCCGCAGTACTGTGTTGGTCATCAGATGTTTCGGGGATTGTACATACTACTATCACTTTATAGAAAACTACCTGGAACATGTATATTAACACCACTGCTACAGATATTATAGTACCgtttcataaacacacacagttggCAGTTGTATATTTGGACTCAGTTTTTGATAGTTGCATTTTTCTTAGATGCTTCATCTAAAGACATGGAAAACCTTTTAGAGCATTAAGTGTTTTTAGTTTGACATCCTCGACATTCATTTGAGTTCATGTTGTGGTTTGGAAAAAATGTATAAGACGTTCtttgtttgaaaaataaataaaaaatgtatgcaaa
>TCONS_00030858
TGCTTATTGCTTGTCGACGTTAACGGCTTAATTAGCACGAAATGGTTTAAATGTCACAATCTCGCCGACATTGATCTCCGAGAAAAGACGTGGTGTATGAAGATGACACAGACGGTCCAGACAAATGGGGTTCAACCCCTCAGCAAGACCTGGGAGCTCAGTCTATATGAATTACAGAGAACTCCACAGGAGGCCATCACGGATGGTCTGGAGATTGCAGTGTCCCCACGCAGCCTGCACAGTGAGCTTATGTGTCCCATCTGCCTGGACATGCTGAAGAACACTATGACCACCAAGGAATGCCTGCACCGTTTCTGTGCCGACTGCATCATCACTGCTCTCAGATCAGGG
>TCONS_00030859
TACAGAAAAGACGTGGTGTATGAAGATGACACAGACGGTCCAGACAAATGGGGTTCAACCCCTCAGCAAGACCTGGGAGCTCAGTCTATATGAATTACAGAGAACTCCACAGGAGGCCATCACGGATGGTCTGGAGATTGCAGTGTCCCCACGCAGCCTGCACAGTGAGCTTATGTGTCCCATCTGCCTGGACATGCTGAAGAACACTATGACCACCAAGGAATGCCTGCACCGTTTCTGTGCCGACTGCATCATCACTGCTCTCAGATCAGGGAATAAGGAGTGTCCAACATGCAGAAAGAAGCTGGTGTCTAAGCGCTCTCTTCGTCCAGACCCTAACTTTGACGCTCTGATCAGTAAGATCTACCCCAGCAGAGACGAATACGAAGCCCACCAGGAGAGAGTGCTGGCCCGCATCAGCAAACACAACAACCAGCAGGCGCTCAGCCACAGTATCGAAGAAGGCCTAAAAATCCAGGCCATGAACAGACTGCAGCGGGGGAAGAAGCATCAAATTGAAAACGGCAGCGGGGCAGAGGACAATGGGGACAGTTCACATTGCAGCAATGCATCAGTGCACAGTAACCAAGAGGCTGGACCCAGCATCAAACGAACCAAAACCTCAGATGACTCTGGACTGGACATGGACAATGCCACTGAGAATGGAGGAGGAGACATTGCGCTGGATGGAGTCAGCGAGATTGAGCTCGTGTTTCGTCCTCACCCAACGCTGATGGAGAAAGAAGACGCCGCTCAGACAAGGTACATCAAGACTTCAGGGAACGCCACAGTGGACCACCTTTCCAAATACTTGGCTGTCAGATTGGCTCTGGAGGAAATGCGCAAGAATGGAGAGGCAAGCCCCATCAATGTAGAGGCCGCCAGTGAAAAACAGTACACAATCTACATCCCTACAGCAAGCAACCAGTTCACAGTCCTGAATGGCTCTTTCTCCCTGGAGCTGGTGAGCGAAAAGTACTGGAAGGTCAACAAGCCCATGGAGTTGTACTTCGCCCCAACGAAGGAACACAAATGAGCCCTGTGAGAC

Function

symbol description
rnf2 Predicted to enable chromatin binding activity and ubiquitin protein ligase activity. Acts upstream of or within several processes, including animal organ morphogenesis; negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator; and pectoral fin development. Predicted to be located in nuclear body. Predicted to be part of MLL1 complex and PRC1 complex. Is expressed in brain; eye; gonad; muscle; and pectoral fin. Orthologous to human RNF2 (ring finger protein 2).

GO:

id name namespace
GO:0035518 histone H2A monoubiquitination biological_process
GO:0032330 regulation of chondrocyte differentiation biological_process
GO:0036353 histone H2A-K119 monoubiquitination biological_process
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0009948 anterior/posterior axis specification biological_process
GO:0033339 pectoral fin development biological_process
GO:0048701 embryonic cranial skeleton morphogenesis biological_process
GO:0060042 retina morphogenesis in camera-type eye biological_process
GO:1902254 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator biological_process
GO:0000278 mitotic cell cycle biological_process
GO:0031519 PcG protein complex cellular_component
GO:0071339 MLL1 complex cellular_component
GO:0000151 ubiquitin ligase complex cellular_component
GO:0035102 PRC1 complex cellular_component
GO:0005634 nucleus cellular_component
GO:0016604 nuclear body cellular_component
GO:0005694 chromosome cellular_component
GO:0016740 transferase activity molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003682 chromatin binding molecular_function
GO:0061630 ubiquitin protein ligase activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-030131-5243 Predicted to enable chromatin binding activity and ubiquitin protein ligase activity. Acts upstream of or within several processes, including animal organ morphogenesis; negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator; and pectoral fin development. Predicted to be located in nuclear body. Predicted to be part of MLL1 complex and PRC1 complex. Is expressed in brain; eye; gonad; muscle; and pectoral fin. Orthologous to human RNF2 (ring finger protein 2).

Ensembl:

ensembl_id ENSDARG00000010381

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00030857 False 2009 mRNA 0.46 7 23351454 23361933
TCONS_00030858 False 351 mRNA 0.50 3 23351533 23355705
TCONS_00030859 True 1048 mRNA 0.52 6 23352302 23361009

Neighbor

gene id symbol gene type direction distance location
XLOC_015415 kifap3b coding upstream 57953 23222939 ~ 23293501 (+)
XLOC_015416 BX548024.3 coding upstream 93557 23257777 ~ 23257897 (+)
XLOC_015414 NA coding upstream 166650 23156012 ~ 23184804 (+)
XLOC_015413 si:dkey-218h11.6 coding upstream 219320 23130389 ~ 23132134 (+)
XLOC_015412 mfsd12a coding upstream 248305 23081247 ~ 23103149 (+)
XLOC_015418 NA coding downstream 44520 23406453 ~ 23479246 (+)
XLOC_015419 NA coding downstream 52950 23414883 ~ 23421047 (+)
XLOC_015420 NA coding downstream 88839 23450772 ~ 23451401 (+)
XLOC_015421 BX470197.1 coding downstream 120865 23482798 ~ 23484348 (+)
XLOC_015422 NA coding downstream 179794 23541727 ~ 23609276 (+)
XLOC_015410 NA non-coding upstream 324476 23025321 ~ 23026978 (+)
XLOC_015408 NA non-coding upstream 359425 22985130 ~ 22992029 (+)
XLOC_015407 NA non-coding upstream 435070 22911192 ~ 22916384 (+)
XLOC_015423 NA non-coding downstream 188253 23550186 ~ 23557515 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000004_06074774_06078306 RNF2.L, RNF2 coding CI01000004 null 6074669 ~ 6079254 (-)
bowfin (Amia calva) AMCG00005079 rnf2,LOC107677769,LOC107718134,LOC107693737 coding CM030140.1 CM030140.1 14800105 ~ 14805904 (+)