RetrogeneDB ID: retro_mmus_622

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:22153282..22154416(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_622
ATGTCCGCGTCAGGGCTTAAGGCCGAGCTGAAGTTCCTGGCGTCCATCTTCGACAAGAACCTCGAGCGATTCCGCATCAT
CAGCTGGAAGCTGGACGAGCTGCACTGCCAGTTCCTGGTGCCGCAGCCGCCACCACCGCCGGGCAGCTCGCTTTCGCCGC
CGCCGCCGCTCACACTTCACTGCAACATCACGGAATCTTACCCATCTTCATCACCAATATGGTTTGTGGACTCTGATGAC
CCAAATCTGACATCAGTTCTGGAACGCTTAGAAGATACTAAGAACAACAGTTCGCTCCGTCAGCAATTGAAGTGGTTGAT
ATGTGACCTCTGCAGATTATATAACCTTCCTAAGCACCTGGATGTTGAGATGCTAGATCAACCCTTACCCACGGGTCAGA
ATGGGACAACTGAAGAAGTAACTTCAGAAGAAGAGGAAGAGGAGGAGATGGCTGAAGATATAGAAGACTTGGATCACTAT
GAGATGAAGGAAGAAGAACCTATTAATGGGGAAAAGTCAGAGGATGAAGGGATTGAAAAAGAAAATTTGGCAATATTAGA
GAAAATCAGGAAGACTCAATGGCAAGACCATTTAAATGGTGCAGTGTCTGGGTCAGTACAAGCATCAGACAGACTGATGA
AGGAGCTCAGGGACGTCTACAGATCACAGAGCTACAAGGCAGGGATTTATTCAGTGGAGCTAATAAATGACAGCTTATAT
GACTGGCATGTCAAACTACACAAGGTTGACTCTGATAGTCCTTTGCACAGTGATCTTCAGATCTTAAAAGAAAAAGAAGG
CATAGAATATATTTTGCTTAACTTCTCTTTTAAGGATAATTTTCCATTTGATCCTCCGTTTGTTAGAGTGGTGTTACCTG
TTCTCTCAGGAGGGTATGTGTTGGGTGGAGGAGCACTGTGTATGGAACTTCTCACAAAACAGGGCTGGAGCAGTGCCTAC
TCAATAGAATCTGTCATCATGCAGATCAATGCCACCTTAGTGAAAGGCAAAGCCCGGGTGCAGTTTGGAGCAAATAAGAA
TCAGTATAATCTAGCACGAGCCCAACAGTCCTATAATTCCATTGTACAGATACATGAGAAAAATGGCTGGTACACACCTC
CAAAGGAAGATGGC

Alignment

ORF - retro_mmus_622 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVSGLKAELKFLASIFDKNHERFRIVSWKLDELHCQFLVPPPPPPPGSSLSPPPPLTLHCNITESYPSS
          MS.SGLKAELKFLASIFDKN.ERFRI.SWKLDELHCQFLVP.PPPPPGSSLSPPPPLTLHCNITESYPSS
Retrocopy MSASGLKAELKFLASIFDKNLERFRIISWKLDELHCQFLVPQPPPPPGSSLSPPPPLTLHCNITESYPSS

Parental  SPIWFVDSDDPNLTSVLERLEDTKNNSSLRQQLKWLICDLCRLYNLPKHLDVEMLDQPLPTGQNGTTEEV
          SPIWFVDSDDPNLTSVLERLEDTKNNSSLRQQLKWLICDLCRLYNLPKHLDVEMLDQPLPTGQNGTTEEV
Retrocopy SPIWFVDSDDPNLTSVLERLEDTKNNSSLRQQLKWLICDLCRLYNLPKHLDVEMLDQPLPTGQNGTTEEV

Parental  TSEEEEEEEMAEDIEDLDHYEMKEEEPINGKKSEDEGIEKENLAILEKIRKTQRQDHLNGAVSGSVQASD
          TSEEEEEEEMAEDIEDLDHYEMKEEEPING.KSEDEGIEKENLAILEKIRKTQ.QDHLNGAVSGSVQASD
Retrocopy TSEEEEEEEMAEDIEDLDHYEMKEEEPINGEKSEDEGIEKENLAILEKIRKTQWQDHLNGAVSGSVQASD

Parental  RLMKELRDVYRSQSYKAGIYSVELINDSLYDWHVKLHKVDSDSPLHSDLQILKEKEGIEYILLNFSFKDN
          RLMKELRDVYRSQSYKAGIYSVELINDSLYDWHVKLHKVDSDSPLHSDLQILKEKEGIEYILLNFSFKDN
Retrocopy RLMKELRDVYRSQSYKAGIYSVELINDSLYDWHVKLHKVDSDSPLHSDLQILKEKEGIEYILLNFSFKDN

Parental  FPFDPPFVRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYN
          FPFDPPFVRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYN
Retrocopy FPFDPPFVRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYN

Parental  LARAQQSYNSIVQIHEKNGWYTPPKEDG
          LARAQQSYNSIVQIHEKNGWYTPPKEDG
Retrocopy LARAQQSYNSIVQIHEKNGWYTPPKEDG

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	0.23 RPM	40.44 RPM
SRP007412_cerebellum	0.35 RPM	34.87 RPM
SRP007412_heart	0.03 RPM	19.71 RPM
SRP007412_kidney	0.10 RPM	23.95 RPM
SRP007412_liver	0.05 RPM	15.84 RPM
SRP007412_testis	0.23 RPM	37.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_622 was not detected

EST

No EST(s) were mapped for retro_mmus_622 retrocopy.

TSS

No TSS is located nearby retro_mmus_622 retrocopy 5' end.

Lab

retro_mmus_622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_622 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,