RetrogeneDB ID:

retro_mmus_83

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:153498453..153500370(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000050148
Aliases:Ubqln2, Chap1, Dsk2, HRIHFB2157, Plic-2, Plic2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Ubqln1
Ensembl ID:ENSMUSG00000005312
Aliases:Ubqln1, 1110046H03Rik, 1810030E05Rik, AU019746, C77538, D13Ertd372e, Da41, Dsk2, Plic-1, Plic1, Xdrp1
Description:ubiquilin 1 [Source:MGI Symbol;Acc:MGI:1860276]


Retrocopy-Parental alignment summary:






>retro_mmus_83
ATGGCTGAGAACGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCGGCGGCCCCAGGCGCGGCCAGCCCGCC
GGCCGAGCCCAAAATCATCAAAGTCACTGTGAAGACCCCCAAAGAGAAGGAGGAGTTCGCGGTGCCCGAGAACAGCACCG
TGCAGCAGTTCAAGGAAGCGATTTCCAAACGCTTCAAATCGCAGACCGATCAGCTCGTGCTGATTTTCGCCGGAAAGATC
CTGAAAGATCAAGATACCTTGATGCAGCATGGCATCCATGATGGACTGACTGTTCACCTGGTTATCAAAAGCCAGAACCG
TCCGCAGGGCCAGGCCACCACGCAGCCCAGCACGACTGCGGGAACGAGCACGACGACCACGACCACCACCACGGCGGCGG
CGCCGGCGGCGACGACATCATCGGCTCCCAGGAGTAGCTCCACACCTACCACCACGAATAGCAGCTCCTTTGGGCTGGGA
AGCCTTTCCAGCCTTAGTAACCTGGGCTTGAACTCGCCCAACTTCACCGAGCTTCAGAACCAGATGCAGCAGCAGCTCCT
GGCCAGCCCTGAGATGATGATCCAGATCATGGAAAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTGATGAGGC
AGCTCATCATGGCCAATCCACAGATGCAACAATTGATCCAGAGAAACCCAGAAATCAGCCACCTACTGAACAACCCAGAT
ATAATGAGGCAGACGCTGGAAATCGCCAGGAATCCTGCCATGATGCAAGAGATGATGCGAAATCAAGACCTGGCTCTCAG
TAATCTCGAAAGCATCCCAGGTGGCTACAATGCTCTGCGGCGCATGTACACTGACATTCAAGAACCTATGCTGAATGCCG
CACAGGAGCAGTTTGGGGGCAACCCGTTTGCCACGGTGGGGAGCAGTTCCACCTCAGGGGAAGGTACTCAGCCCTCCCGC
ACGGAGAATCGTGATCCGCTGCCCAATCCTTGGGCACCACCGCCAACAACCCAGACGGCTGCGACCACCACCACCACCAC
GACCACAAGCAGTGGCAGTGGCTCTGGCAGCAGCTCCAGCAGCACCACCGCCGGGAACACCATGGCTGCAGCTAATTACG
TGGCTAGCATCTTCAGCACCCCAGGAATGCAGAGCCTGCTGCAGCAGATAACTGAGAATCCCCAGCTGATTCAGAATATG
CTGTCTGCGCCCTACATGCGGAGCATGATGCAGTCGCTGAGCCAGAATCCAGATATGGCGGCCCAGATGATGCTGAGTAG
CCCGCTGTTCACTTCGAATCCTCAGCTGCAGGAGCAGATGCGTCCACAGCTCCCGAATTTCCTGCAGCAGATGCAGAATC
CAGAAACCATCGCGGCCATGTCAAACCCGAGAGCGATGCAAGCGCTAATGCAGATCCAGCAGGGGCTACAGACTCTAGCC
ACTGAAGCACCTGGCCTCATTCCCAGCTTCGCTCCAGGTGTGGGGATGGGAGTGCTGGGAACCGCCATAACCCCTGTGGG
CCCAGTCACTCCCATAGGGCCCATCGGCCCTATAGTTCCTTTCACCCCCATAGGCCCCATCGGGCCTATAGGACCCACTG
GCCCTGCAAGCTCCCCCGGCTCCACCGGCACTGGCATCCCGCCTGCAACCACTGTGTCCAGCTCTGCACCTACTGAAACC
ATAAGTCCAACCTCGGAATCTGGACCCAACCAGCAGTTCATTCAACAAATGGTGCAGGCTCTCACTGGAGGAAGCCCTCC
ACAGCCGCCGAATCCTGAAGTGAGATTTCAGCAGCAACTGGAACAGCTCAACGCCATGGGGTTCTTAAACCGCGAAGCAA
ACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAACGCGGCCATTGAGAGGCTGCTGGGCTCTCAGCCATCCTAA

ORF - retro_mmus_83 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.71 %
Parental protein coverage: 66.67 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTNAPGSTVTSSPAPDSNPTSGSAANSSFGVGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQI
T.A.....T.S.AP.S..T......SSF...GLG.L..LS.LGLN..NF.ELQ.QMQ.QLL..PEMM.QI
RetrocopyTTAAAPAATTSSAPRSSSTPTTTNSSSF---GLGSLSSLSNLGLNSPNFTELQNQMQQQLLASPEMMIQI
ParentalMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRAL
MENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.AL
RetrocopyMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLAL
ParentalSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASLVSSSSSAEGTQPSRTENRDPLPNPWAPQTS
SNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFA...SSS.S.EGTQPSRTENRDPLPNPWAP...
RetrocopySNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFATVGSSSTSGEGTQPSRTENRDPLPNPWAPPPT
ParentalQSSPASGTTGSTTNTMSTSGGTATSTPAGQSTSGPSLVPGAGASMFNTPGMQSLLQQITENPQLMQNMLS
....A..TT..TT...S.SG....ST.AG........V....AS.F.TPGMQSLLQQITENPQL.QNMLS
RetrocopyTQTAATTTTTTTTSSGSGSGSSSSSTTAGNTMAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLS
ParentalAPYMRSMLQSLSQNPDLAAQMMLNNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQI
APYMRSM.QSLSQNPD.AAQMML..PLF..NPQLQEQMR.QLP.FLQQMQNP.T..AMSNPRAMQAL.QI
RetrocopyAPYMRSMMQSLSQNPDMAAQMMLSSPLFTSNPQLQEQMRPQLPNFLQQMQNPETIAAMSNPRAMQALMQI
ParentalQQGLQTLATEAPGLIPGFTPGLAAGNSGGSSGTNAPST
QQGLQTLATEAPGLIP.F.PG...G..G.......P.T
RetrocopyQQGLQTLATEAPGLIPSFAPGVGMGVLGTAITPVGPVT

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
SRP007412_brain 124 .99 RPM 168 .33 RPM
SRP007412_cerebellum 106 .95 RPM 186 .97 RPM
SRP007412_heart 22 .54 RPM 60 .70 RPM
SRP007412_kidney 20 .89 RPM 140 .12 RPM
SRP007412_liver 10 .38 RPM 150 .20 RPM
SRP007412_testis 8 .64 RPM 108 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_83 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A X:153497811..153498499
ENCFF001YJZ POLR2A X:153497245..153498777
ENCFF001YKA POLR2A X:153497373..153498559

EST - click to see more details

41 EST(s) were mapped to retro_mmus_83 retrocopy
EST ID Start End Identity Match Mis-match Score
AA030192 153498672 153499107 99.4 432 2 428
AA117575 153499751 153499923 98.9 170 2 168
AI509123 153498677 153499107 98.9 425 3 418
AI391077 153498491 153498899 99.8 407 1 406
AI413170 153498472 153498865 100 393 0 393
AI413921 153498472 153498931 99.4 459 0 458
AI414229 153498444 153498783 100 339 0 339
AI430809 153498444 153498756 99.4 310 2 308
AV480727 153499416 153499929 99.9 510 1 507
AW046593 153498445 153498835 96.2 378 12 365
AW050079 153498445 153498800 100 355 0 355
AW244687 153499180 153499479 99.7 298 1 297
BE381327 153498739 153499361 98 618 2 609
BE864671 153498979 153499431 99.4 448 3 445
BE950186 153498445 153498924 99 477 2 474
BE950766 153498445 153498913 99.2 464 4 460
BE995880 153498444 153498752 100 308 0 308
BF137260 153498870 153499653 98.5 721 5 699
BG228726 153498480 153498938 99.4 458 0 457
BG694578 153498915 153499367 98.1 443 9 434
BM944608 153499135 153499744 99.9 606 1 603
BQ715304 153498799 153499558 97.8 754 0 741
BQ769737 153498591 153499292 100 697 0 696
BU614196 153499186 153499768 100 582 0 582
BU702010 153498885 153499598 100 713 0 713
CA324121 153498512 153499250 100 737 0 737
CA324233 153498410 153499219 100 809 0 809
CA530125 153498844 153499444 99.9 599 1 598
CB246615 153498517 153499250 100 732 0 732
CD353970 153498660 153499335 100 673 0 673
CD553142 153499090 153499209 100 119 0 119
CF736553 153498645 153499353 100 705 0 705
CN529501 153498571 153499385 99.8 803 1 800
CN530225 153498571 153499199 100 628 0 628
CV562253 153498784 153499442 100 658 0 658
CX206222 153499374 153499918 99.3 543 1 541
CX211713 153499111 153499672 99.7 559 2 557
CX733159 153499083 153499725 99.9 641 1 640
CX733792 153498948 153499575 99.9 626 1 625
W30442 153498535 153498899 99.8 361 0 358
W57195 153499435 153499830 100 395 0 395

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_155947163 libraries275 libraries570 libraries60 libraries4 libraries
TSS #2 TSS_15594869 libraries65 libraries658 libraries172 libraries108 libraries
TSS #3 TSS_1559493 libraries0 libraries1 library13 libraries1055 libraries

The graphical summary, for retro_mmus_83 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_83 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_83 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 ENSMUSG00000005312 1 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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