RetrogeneDB ID: retro_mmus_3421

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:12937501..12938125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083307
• 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_3421
AAAAAGTCAGAGGATGAAGGGCTTGAGAAAGAGCATTTGGCAATATTAGAGAATATCAAGAAGAGCCAAAGGCAAGAGCA
TTTGAATGGTACCGTGTCTGGCTCGGTGCATGCTTCAAACAGACTTATGAAAGAACTCAGAGATATATACAGATCGCAGA
GCTACAAATCGGGGACTTATTCCGTGGAACTGATAAACGACAGCTTATATGACTGGCACGTTAAACTGAGGAAGGTTGAC
CCCGATAGTCCCTTGTACGGTGACCTTCAGCTCTTGAATGAAAAAGAAGGCATTGACTATATTTTGCTTAACTTCTCTTT
CAAAGATAACTTTCCGTTTGATCCTCCATTTGTTCGCGTCGAGTTGCCTATTCTCTCTGGAGGGTATGTTTTGGGTGGAG
GGGCGTTGTGTATGGAACTGCTCACCAAACAGGGCTGGAGCAGCGCCTACTCCATTGAATCAGTCATCATGCAGATCAAT
GCCACCTTAGTCAAAGGCAAGGCCAGGGTGCGCTTTGGAGCAGATAAGAATCAATATAATCTAGAAACAGCCCAACAGTC
CTATGACTCCGTCGTGCAGATGCATGAGAAAAAGGGCTGGTTCACTCCTCCAAAGGAAGATGGG

Alignment

ORF - retro_mmus_3421 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 55.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKSEDEGIEKENLAILEKIRKTQRQDHLNGAVSGSVQASDRLMKELRDVYRSQSYKAGIYSVELINDSLY
          KKSEDEG.EKE.LAILE.I.K.QRQ.HLNG.VSGSV.AS.RLMKELRD.YRSQSYK.G.YSVELINDSLY
Retrocopy KKSEDEGLEKEHLAILENIKKSQRQEHLNGTVSGSVHASNRLMKELRDIYRSQSYKSGTYSVELINDSLY

Parental  DWHVKLHKVDSDSPLHSDLQILKEKEGIEYILLNFSFKDNFPFDPPFVRVVLPVLSGGYVLGGGALCMEL
          DWHVKL.KVD.DSPL..DLQ.L.EKEGI.YILLNFSFKDNFPFDPPFVRV.LP.LSGGYVLGGGALCMEL
Retrocopy DWHVKLRKVDPDSPLYGDLQLLNEKEGIDYILLNFSFKDNFPFDPPFVRVELPILSGGYVLGGGALCMEL

Parental  LTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYNLARAQQSYNSIVQIHEKNGWYTPPKEDG
          LTKQGWSSAYSIESVIMQINATLVKGKARV.FGA.KNQYNL..AQQSY.S.VQ.HEK.GW.TPPKEDG
Retrocopy LTKQGWSSAYSIESVIMQINATLVKGKARVRFGADKNQYNLETAQQSYDSVVQMHEKKGWFTPPKEDG

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	3.67 RPM	40.44 RPM
SRP007412_cerebellum	2.43 RPM	34.87 RPM
SRP007412_heart	0.62 RPM	19.71 RPM
SRP007412_kidney	0.71 RPM	23.95 RPM
SRP007412_liver	0.16 RPM	15.84 RPM
SRP007412_testis	3.52 RPM	37.28 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_3421 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	X:12936761..12937233
ENCFF001YIJ	POLR2A	X:12936410..12937195
ENCFF001YKA	POLR2A	X:12936534..12937156

EST

No EST(s) were mapped for retro_mmus_3421 retrocopy.

TSS

No TSS is located nearby retro_mmus_3421 retrocopy 5' end.

Lab

retro_mmus_3421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3421 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_297

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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,