RetrogeneDB ID:

retro_rnor_339

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:X:19489168..19491085(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000003099
Aliases:Ubqln2, RGD1563566
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Ubqln1
Ensembl ID:ENSRNOG00000019282
Aliases:Ubqln1, Da41
Description:ubiquilin-1 [Source:RefSeq peptide;Acc:NP_446199]


Retrocopy-Parental alignment summary:






>retro_rnor_339
ATGGCTGAGAACGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCTGCGGCCCCAGGCGCGGCCAACCCGCC
AGCCGAGCCCAAAATCATCAAAGTCACTGTGAAGACCCCCAAAGAGAAGGAGGAGTTCGCGGTGCCCGAGAACAGCACCG
TGCAGCAGTTCAAGGAAGCGATTTCTAAACGCTTCAAATCGCAAACCGATCAGCTCGTGCTGATTTTCGCTGGAAAAATC
CTGAAAGATCAAGACACCTTGATCCAGCATGGCATCCATGATGGACTGACTGTTCACCTGGTTATCAAAAGCCAGAACCG
TCCGCAGGGCCAGGCCACCACGCAGCCCAGCACTACTGCGGGAACGAGCACGACGACCACGACCACCACCACGGCGGCGG
CGCCGCCGGCGGCGACTACATCATCGGCTCCCAGGTGTAGCACCACAGCTACTACCACAAATAGCAGCAACTTGGGGCTC
GGAAGCCTTGCCAGCCTTGGTAACCTGGGTTTGAACTCGTCCAACTTCACCGAGCTTCAGAACCAGATGCAGCAGCAGCT
CTTGGCCAGCCCCGAGATGATGATCCAGATCATGGAAAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTGATGA
GGCAGCTCATCATGGCCAATCCACAGATGCAACAATTGATCCAGAGAAACCCAGAAATCAGCCACCTACTGAACAACCCA
GATATAATGAGGCAGACTCTCGAAATCGCCAGGAATCCTGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCT
CAGTAATCTCGAAAGCATCCCAGGTGGCTACAATGCTCTGCGGCGCATGTACACTGACATTCAAGAACCCATGCTGAATG
CCGCACAGGAGCAGTTTGGGGGCAATCCGTTTGCCACGGTGGGGAGCAGTTCCTCCTCAGGGGAAGGTACTCAGCCTTCC
CGCACGGAGAATCGGGATCCGCTGCCTAATCCTTGGGCACCACCGCCAACTACCCAGACCTCTGCGACGACCACCACCAC
GACCACAAGCAGTGGCACTGTGGCTGGCAGCAACACCAGCAGCACTACGGCCGGGAACACCATGGCTGCAGCTAATTATG
TGGCCAGCATCTTCAGCACCCCAGGAATGCAGAGCCTGCTGCAGCAGATAACTGAAAATCCCCAGCTGATTCAGAATATG
CTGTCTGCACCCTACATGAGAAGCATGATGCAGTCGCTGAGCCAGAATCCAGATATGGCTGCCCAGATGATGCTGAGTAG
CCCACTGTTTACGGCGAATCCTCAGCTGCAGGAGCAGATGCGTCCACAGCTCCCGAATTTCCTGCAGCAGATGCAGAGTC
CAGAAACCATCGCGGCCATGTCAAACCCGAGAGCGATGCAAGCGCTACTGCAGATCCAGCAGGGGCTACAGACACTAGCC
ACTGAAGCACCTGGCCTCATTCCAGGCTTCACTCCAGGTGTGGGGGTGGGAGTGCTGGGAACGGCCATAACCCCTGTGGG
CCCAGTCACTCCCATAGGGCCCATCGGTCCTATCGTTCCTTTCACCCCCATAGGCCCCATCGGGCCTATAGGACCCACTG
GCCCTGCCAGCTCCCCTGGCTCGACCGGCACCGGGATCCCGCCTGCAACCACTGTGTCCAGCTCTGCACCTACTGAAACC
ATAAGTCCAACATCAGAATCTGGACCCAGCCAGCAGTTCATTCAGCAAATGGTGCAGGCTCTCACTGGAGGAAGTCCTCC
ACAGCCGCCGAATCCTGAAGTGAGATTTCAGCAGCAACTGGAACAGCTCAACGCCATGGGGTTCTTAAACCGCGAAGCAA
ACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAACGCGGCCATTGAGAGGCTGCTGGGCTCTCAGCCATCCTAA

ORF - retro_rnor_339 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.35 %
Parental protein coverage: 66.15 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSVTSSPAPDSNPTSGPAANSSFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFV
..T.S.AP....T......S.....GLG.LA.L..LGLN..NF.ELQ.QMQ.QLL..PEMM.QIMENPFV
RetrocopyAATTSSAPRCSTTATTTNSSNL---GLGSLASLGNLGLNSSNFTELQNQMQQQLLASPEMMIQIMENPFV
ParentalQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESI
QSMLSNPDLMRQLIMANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESI
RetrocopyQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESI
ParentalPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASLVSSPSSAEGTQPSRTENRDPLPNPWAPQTPQSSPAS
PGGYNALRRMYTDIQEPMLNAAQEQFGGNPFA...SS.SS.EGTQPSRTENRDPLPNPWAP..P.....S
RetrocopyPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFATVGSSSSSGEGTQPSRTENRDPLPNPWAP--PPTTQTS
ParentalGSTGSTTNTVSTSAG-NATSTPAGQGTSGPNLVPGAGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMR
..T..TT....T.AG.N..ST.AG......N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMR
RetrocopyATTTTTTTSSGTVAGSNTSSTTAGNTMAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMR
ParentalSMMQSLSQNPDLAAQMMLNNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQ
SMMQSLSQNPD.AAQMML..PLF..NPQLQEQMR.QLP.FLQQMQ.P.T..AMSNPRAMQALLQIQQGLQ
RetrocopySMMQSLSQNPDMAAQMMLSSPLFTANPQLQEQMRPQLPNFLQQMQSPETIAAMSNPRAMQALLQIQQGLQ
ParentalTLATEAPGLIPGFTPGLAAGNSGGPAGTTAPSTAPG
TLATEAPGLIPGFTPG...G..G.......P.T..G
RetrocopyTLATEAPGLIPGFTPGVGVGVLGTAITPVGPVTPIG

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
SRP017611_brain 109 .21 RPM 113 .38 RPM
SRP017611_kidney 31 .82 RPM 115 .35 RPM
SRP017611_liver 13 .78 RPM 108 .72 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_339 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_339 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_339 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 ENSECAG000000191101 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 ENSRNOG00000019282 1 retrocopy
retro_rnor_339 ,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG000000046961 retrocopy
retro_ttru_1475,


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