RetrogeneDB ID: retro_mmus_1282

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:56010538..56011351(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000058581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2j2
• Ensembl ID: ENSMUSG00000023286
• Aliases: Ube2j2, 1200007B18Rik, 2400008G19Rik, 5730472G04Rik, AL022923, NCUBE-2, Ubc6, Ubc6p
• Description: ubiquitin-conjugating enzyme E2J 2 [Source:MGI Symbol;Acc:MGI:2153608]

Sequence

>retro_mmus_1282
ATGCATCAGGCAAAAGCCCTTGATTCTGCCAGAAAGATGAGCAATAACAGCAATAAGAGAGCTCCAACAACAGCAACACA
AAGGTTGAAGCAGGACTACCTTCGAATTAAGAAAGACCCAGTGCCTTACATCTGTGCAGAGCCCCTCCCTTCAAATATTC
TTGAATGGCATTATGTTGTCCGAGGCCCTGAGATGACTCCTTATGAAGGTAGCTATTATCATGGAAAACTAATTTTTCCC
AGAGAATTTCCATTTAAGCCTCCTAGTATTTACATGATAACCCCCAATGGAAGATTTAAGTGCAACACGAGGCTGTGTCT
CTCCATCACAGATTTCCACCCAGATACATGGAATCCAGCGTGGTCCGTCTCCACCATTCTAACAGGGCTCCTGAGCTTTA
TGGTGGAGAAAGGCCCCACCCTGGGAAGCATAGAGACGTCGGACTTCACGAAAAAACAGCTGGCAGCACAGAGTCTAGTG
TTTAATTTAAAAGATAAAGTCTTTTGTGAATTATTTCCTGAAGTTGTGGAGGAAATTAAACAGAAACAGAAAGCACAAGA
TGAACTAAGTAACAGGCCCCAGAATCTTCCTTTGCCAGACGTGGTTCCTGATGGGGAGCTGCACGGTGGCCAGCATGGGA
TCCAGCTCCTCAATGGGCACGCACCCGCTGCTGGCCCCAACCTCGCTGGGCTCCCACAGGCCAACAGGCATCATGGACTC
CTGGGCGGCGCGTTGGCGAACTTGTTTGTTATAGTTGGGTTTGCAGCCTTTGCCTACACGGTCAAGTACGTGCTGAGAAG
CATAGCACAGGAG

Alignment

ORF - retro_mmus_1282 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHQAKALDSARKMSNNSNKRAPTTATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEG
          MHQAKALDSARKMSNNSNKRAPTTATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEG
Retrocopy MHQAKALDSARKMSNNSNKRAPTTATQRLKQDYLRIKKDPVPYICAEPLPSNILEWHYVVRGPEMTPYEG

Parental  GYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPT
          .YYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPT
Retrocopy SYYHGKLIFPREFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPT

Parental  LGSIETSDFTKKQLAAQSLVFNLKDKVFCELFPEVVEEIKQKQKAQDELSNRPQNLPLPDVVPDGELHRG
          LGSIETSDFTKKQLAAQSLVFNLKDKVFCELFPEVVEEIKQKQKAQDELSNRPQNLPLPDVVPDGELH.G
Retrocopy LGSIETSDFTKKQLAAQSLVFNLKDKVFCELFPEVVEEIKQKQKAQDELSNRPQNLPLPDVVPDGELHGG

Parental  QHGIQLLNGHAPAAGPNLAGLPQANRHHGLLGGALANLFVIVGFAAFAYTVKYVLRSIAQE
          QHGIQLLNGHAPAAGPNLAGLPQANRHHGLLGGALANLFVIVGFAAFAYTVKYVLRSIAQE
Retrocopy QHGIQLLNGHAPAAGPNLAGLPQANRHHGLLGGALANLFVIVGFAAFAYTVKYVLRSIAQE

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	0.02 RPM	16.82 RPM
SRP007412_cerebellum	0.00 RPM	17.50 RPM
SRP007412_heart	0.06 RPM	15.22 RPM
SRP007412_kidney	0.08 RPM	15.05 RPM
SRP007412_liver	0.05 RPM	15.02 RPM
SRP007412_testis	0.23 RPM	36.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1282 was not detected

EST

No EST(s) were mapped for retro_mmus_1282 retrocopy.

TSS

No TSS is located nearby retro_mmus_1282 retrocopy 5' end.

Lab

retro_mmus_1282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1282 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006403	1 retrocopy	retro_meug_1459,
Mus musculus	ENSMUSG00000023286	1 retrocopy	retro_mmus_1282 ,
Ochotona princeps	ENSOPRG00000002927	1 retrocopy	retro_opri_669,
Rattus norvegicus	ENSRNOG00000019749	1 retrocopy	retro_rnor_2629,