RetrogeneDB ID:

retro_ecab_1063

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:42841867..42843322(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000017595
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSECAG00000019110
Aliases:None
Description:ubiquilin 1 [Source:HGNC Symbol;Acc:12508]


Retrocopy-Parental alignment summary:






>retro_ecab_1063
ATGGCTGAGAACGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGTGGCCCTGCTTCGGCCCAAGGCCCTGCCTCTGCTCC
GGCCGAGCCCAAAATCATCAAAGTCACTGTGAAGACCCCCAAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAATAGCTCAG
TCCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCACGGCATCCATGATGGACTGACTGTTCACCTTGTCATCAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACACAGCCTAGTAATGCCGCGGGAACTAATACTACCTCCCCGTCGACTCCCAGGAATAACTCCA
CACCTCTTTCCACAAATAGCAACCCATTTGGTTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCAACCAACTTCTCTGAGCTCCAGAACCAGATGCAGCAGCAGCTCCTGTCCAGCCCTGAGATGATGATCCAAATCATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTAATGAGGCAGCTCATTATGGCCAATCCACAGATGCAACAGT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACCCTGGAAATAGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAGGACCTGGCTCTCAGCAATCTCGAAAGCATCCCAGGTGGCTACAATGC
CCTGCGGCGCATGTACACTGACATTCAAGAACCCATGCTGAATGCCGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CGGTGGGGAGCAGTTCTTCCTCTGGGGAAGGCACGCAGCCTTCTCGCACAGAAAATCGAGATCCACTACCCAATCCATGG
GCACCACCACCGGCTACCCAGAGTTCTGCGACCACCAGCACAACCTCAAGCAGTGGCAGTGGCAGTGGCAGTGGGTCTGG
TAGTAGCTCCACCAGTGCTACCGGGAACACCGTGGCTGCAGCCAATTATGTTGCCAGCATCTTCAGTACCCCAGGAATGC
AGAGCTTACTGCAACAGATAACTGAAAACCCCCAGCTGATCCAGAATATGCTGTCTGCGCCCTACATGAGAAGCATGATG
CAGTCGCTGAGCCAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCCGTGTTTACTGCAAATCCTCAGCTGCA
GGAGCAGATGCGTCCCCAGCTCCCGGCTTTCCTACAGCAGATGCAGAATCCAGACACACTCTCAGCTATGTCAAACCCAA
GAGCAATGCAGGCTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTCATTCCAAGCTTC
GCTCCAGGTGTAGGG

ORF - retro_ecab_1063 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.87 %
Parental protein coverage: 82.96 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAENSESGGPPSSQDSAAAAEGAGATAAASAEPKIMKVTVKTPK-KEDFAVPENSSVQQFKEEISKRFKS
MAEN.ES.GPP......A.A.G....A.A.AEPKI.KVTVKTPK.KE.FAVPENSSVQQFKE.ISKRFKS
RetrocopyMAENGESSGPPRPSRGPASAQGP---ASAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKS
ParentalHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTSGSGVTTSSAPNSNSTSGS
.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N..G...T..S.P..NST..S
RetrocopyQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSPSTPRNNSTPLS
ParentalATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIMA
..SNPFGLG.LGGLAGLSSLGL..TNFSELQ.QMQ.QL.S.PEMM.QIMENPFVQSMLSNPDLMRQLIMA
RetrocopyTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQNQMQQQLLSSPEMMIQIMENPFVQSMLSNPDLMRQLIMA
ParentalNPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQE
NPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQE
RetrocopyNPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQE
ParentalPMLSAAQEQFGGNPFASLVSSTSSGEGSQPSRTENRDPLPNPWAPQASQGSSASGGTASAVGGTGGSAAS
PML.AAQEQFGGNPFAS..SS.SSGEG.QPSRTENRDPLPNPWAP.....SSA...T.S...........
RetrocopyPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTSXXXXXXXXXSG
ParentalGTAGQSSTAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLNN
.................AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN.
RetrocopySSSTSATGNTVAAANYVASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNS
ParentalPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLG
P.F..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.F.PG.G
RetrocopyPVFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFAPGVG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP021940_articular_cartilage 21 .07 RPM 63 .40 RPM
SRP021940_cerebellum 104 .70 RPM 154 .81 RPM
SRP021940_embryo 66 .44 RPM 127 .40 RPM
SRP021940_placental_villous 10 .54 RPM 116 .00 RPM
SRP021940_synovial_membrane 21 .25 RPM 58 .14 RPM
SRP021940_testis 3 .07 RPM 145 .02 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_1063 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_1063 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1063 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148272 retrocopies
retro_btau_1087, retro_btau_188,
Canis familiaris ENSCAFG000000014351 retrocopy
retro_cfam_236,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG000000048491 retrocopy
retro_cpor_113,
Dasypus novemcinctus ENSDNOG000000126871 retrocopy
retro_dnov_14,
Dipodomys ordii ENSDORG000000152661 retrocopy
retro_dord_680,
Equus caballus ENSECAG00000019110 1 retrocopy
retro_ecab_1063 ,
Echinops telfairi ENSETEG000000028221 retrocopy
retro_etel_39,
Felis catus ENSFCAG000000150491 retrocopy
retro_fcat_83,
Homo sapiens ENSG000001350181 retrocopy
retro_hsap_58,
Myotis lucifugus ENSMLUG000000020362 retrocopies
retro_mluc_1774, retro_mluc_33,
Mustela putorius furoENSMPUG000000020281 retrocopy
retro_mputfur_55,
Mus musculus ENSMUSG000000053121 retrocopy
retro_mmus_83,
Nomascus leucogenys ENSNLEG000000033061 retrocopy
retro_nleu_31,
Otolemur garnettii ENSOGAG000000129471 retrocopy
retro_ogar_276,
Pongo abelii ENSPPYG000000193231 retrocopy
retro_pabe_87,
Pan troglodytes ENSPTRG000000210551 retrocopy
retro_ptro_93,
Rattus norvegicus ENSRNOG000000192821 retrocopy
retro_rnor_339,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG000000046961 retrocopy
retro_ttru_1475,


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