RetrogeneDB ID: retro_mmus_156

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:136400714..136401830(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000045291
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ube2q2
• Ensembl ID: ENSMUSG00000032307
• Aliases: Ube2q2, 3010021M21Rik
• Description: ubiquitin-conjugating enzyme E2Q (putative) 2 [Source:MGI Symbol;Acc:MGI:2388672]

Sequence

>retro_mmus_156
ATGTCGTCAGGTCTTAAGGCTGAGCTGGAGTTCCTAGCATCCATCTTCCACAAGGACCACGAGCGGCTGCGCATCGTGAG
CTGGCACCTGGATGACCTACAGTGTCAGTTCCTGGTGCCGGAGGCAACTGTGGGCAGTCCGCCCTCGCCGCCACCGCTCA
CCCTTCACTGCACCATCACCGAGTCCTACCCATCTTCACCGGCGATGTGGTTCGTGGACTCTGACGATCCAGATCTCACA
TCGATCCTGGAACGCCTGGAAAATTCGAAGCCAGACAGTTCGCTTAGTCAGCAGCTCAAGTGGCTGATCTGTGAACTCTG
CCGCTTATATAACCTGCCTGAGCACCTGGATGTGGAGATGCTGGACCAGCCGGTCCCCATCGCTCAGAAGGCCACCATCA
AAGATGGGTCTTCAGAAGAAGACGAAGATGCATCTTACGGACTGGACGACTCGGATTATTATGACATGAAAGAAGAAGAG
ACGAGTAGTGAGAAAACGTCAGAGAATGAAGGGCTTGAGAAAGAGGATTTGGAAATATTAGAGAATATCCAGAAAAACCT
TTGGCAAAAGAATGCAAGTGGTGCCACGTCTGGCTCAGTGTGTGCTTCAGATAGACTTATGAAAGAACTCAGAGAAATAT
ACAGATCGCAGAGTTACAAATCAGGGACTTTTTCAGTGGAACTGATAAATGACAGCTTATATGACTGGCACGTTAAACTG
AGGAAGGTTGACCCTGATAGTTGCTTGTACAGAGACCTTCAGCGCTTGAAACAAAAAGAAGGCATAGACTATATTTTGCT
TAACTTCTCTTTCAAAGATAACTTTCCGTTTGATCCTCCATTTGTTCGAGTCGTGTTGCCTGTACTCTCTGATGGTTATG
TCTTGGATGGGGGGGCATTGTGTATGGAACTGCTTACCAATCAGGGCTGGAGCAGCGCCTACTCCATAGAATCGGTCATC
TTGCAGATCAATGCCACCTTAGTCAAAGGCAAGGCCAGGGTGCGCTTTGGAGTAGATAATCACTATACTGAACAAGTGGC
TAGACGGGTCTATAAATCCATGGTGCTGAAGCATGAGAAATCAGGCTGGTTCACTCCTCCACAGAAAGATGGGTAA

Alignment

ORF - retro_mmus_156 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLKAELKFLASIFDKNHERFRIVSWKLDELHCQFLVPPPPPPPGSSLSPPPPLTLHCNITESYPSSSPI
          SGLKAEL.FLASIF.K.HER.RIVSW.LD.L.CQFLV..P....GS..SPPP.LTLHC.ITESYPSS...
Retrocopy SGLKAELEFLASIFHKDHERLRIVSWHLDDLQCQFLV--PEATVGSPPSPPP-LTLHCTITESYPSSPAM

Parental  WFVDSDDPNLTSVLERLEDTKNNSSLRQQLKWLICDLCRLYNLPKHLDVEMLDQPLPTGQNGTTEEVTSE
          WFVDSDDP.LTS.LERLE..K..SSL.QQLKWLIC.LCRLYNLP.HLDVEMLDQP.P..Q..T.....SE
Retrocopy WFVDSDDPDLTSILERLENSKPDSSLSQQLKWLICELCRLYNLPEHLDVEMLDQPVPIAQKATIKDGSSE

Parental  EEEEEEMAEDIEDLDHYEMKEEEPINGKKSEDEGIEKENLAILEKIRKTQRQDHLNGAVSGSVQASDRLM
          E.E.........D.D.Y.MKEEE....K.SE.EG.EKE.L.ILE.I.K...Q....GA.SGSV.ASDRLM
Retrocopy EDEDASYG--LDDSDYYDMKEEETSSEKTSENEGLEKEDLEILENIQKNLWQKNASGATSGSVCASDRLM

Parental  KELRDVYRSQSYKAGIYSVELINDSLYDWHVKLHKVDSDSPLHSDLQILKEKEGIEYILLNFSFKDNFPF
          KELR..YRSQSYK.G..SVELINDSLYDWHVKL.KVD.DS.L..DLQ.LK.KEGI.YILLNFSFKDNFPF
Retrocopy KELREIYRSQSYKSGTFSVELINDSLYDWHVKLRKVDPDSCLYRDLQRLKQKEGIDYILLNFSFKDNFPF

Parental  DPPFVRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYNLAR
          DPPFVRVVLPVLS.GYVL.GGALCMELLT.QGWSSAYSIESVI.QINATLVKGKARV.FG...N.Y....
Retrocopy DPPFVRVVLPVLSDGYVLDGGALCMELLTNQGWSSAYSIESVILQINATLVKGKARVRFGVD-NHYTEQV

Parental  AQQSYNSIVQIHEKNGWYTPPKEDG
          A...Y.S.V..HEK.GW.TPP..DG
Retrocopy ARRVYKSMVLKHEKSGWFTPPQKDG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	40.44 RPM
SRP007412_cerebellum	0.00 RPM	34.87 RPM
SRP007412_heart	0.00 RPM	19.71 RPM
SRP007412_kidney	0.19 RPM	23.95 RPM
SRP007412_liver	0.03 RPM	15.84 RPM
SRP007412_testis	0.05 RPM	37.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_156 was not detected

EST

No EST(s) were mapped for retro_mmus_156 retrocopy.

TSS

No TSS is located nearby retro_mmus_156 retrocopy 5' end.

Lab

retro_mmus_156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000032307	3 retrocopies	retro_mmus_156 , retro_mmus_3421, retro_mmus_622,
Oryctolagus cuniculus	ENSOCUG00000022720	1 retrocopy	retro_ocun_1419,