RetrogeneDB ID: retro_mmus_2288

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:108239418..108239911(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083462
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Siva1
• Ensembl ID: ENSMUSG00000064326
• Aliases: Siva1, CD27bp, Siva
• Description: SIVA1, apoptosis-inducing factor [Source:MGI Symbol;Acc:MGI:1353606]

Sequence

>retro_mmus_2288
ATGCCCAAGTGGAGCTGCCCGTTTGCAGACGCAGCCCCGCTCCAACTCAAAGGCCACGTGGGCCTGAAAATGCTGAGCCA
CGGTGTGTTCGCCGAGCGCTACTCACACGAGGTCTTCGAAAGAACCAAGCAGCTCCTTTTCCAAGGGGTTCGGGCCTATA
GAGATCACATATCGAGCGAAGATTTGTTCCGTGAACCACCTGCGGGAGTCACTGAAGTCTGGTGTGGTGGGAGCCCCTCA
AACTGCGAGAGGACAGATGTTGATTGGATCTGATAGCCGACTGACACGGTGCCAAGCTCAGGCCTCAGAAGGTGGCCTTC
CCAGGACAGCGCCCATCGCTTGTTCGTCATGCATAAGATCTGTGGATGGGAAGGCGGTCTGCAGCCAGTGTGAGCGGGCC
CTGTGTGGGCAGTGTGTATACACCTGCTGGGGCTGCAGTGCTTTGGCCTGTGTGCTGTGTGGCCTTGCAGACTATGCTGA
TGATGGTGAGAAG

Alignment

ORF - retro_mmus_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.73 %
• Parental protein coverage: 93.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRSCPFADAAPLQLKVHVGLKELSHGVFAERYSREVFERTKQLLFQGARAYRDHISSED-CSVNHLQE
          MPK.SCPFADAAPLQLK.HVGLK.LSHGVFAERYS.EVFERTKQLLFQG.RAYRDHISSED.CSVNHL.E
Retrocopy MPKWSCPFADAAPLQLKGHVGLKMLSHGVFAERYSHEVFERTKQLLFQGVRAYRDHISSED>CSVNHLRE

Parental  SLKSGVVGAPQPARGQMLIGPDGRLTRCQAQASEGGLPRTAPIACSSCMRSVDGKAVCSQCERALCGQCV
          SLKSGVVGAPQ.ARGQMLIG.D.RLTRCQAQASEGGLPRTAPIACSSC.RSVDGKAVCSQCERALCGQCV
Retrocopy SLKSGVVGAPQTARGQMLIGSDSRLTRCQAQASEGGLPRTAPIACSSCIRSVDGKAVCSQCERALCGQCV

Parental  YTCWGCGALACVLCGLADYADDGEK
          YTCWGC.ALACVLCGLADYADDGEK
Retrocopy YTCWGCSALACVLCGLADYADDGEK

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	0.16 RPM	3.34 RPM
SRP007412_cerebellum	0.00 RPM	3.82 RPM
SRP007412_heart	0.03 RPM	8.59 RPM
SRP007412_kidney	0.21 RPM	5.33 RPM
SRP007412_liver	0.00 RPM	3.88 RPM
SRP007412_testis	0.00 RPM	5.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2288 was not detected

EST

No EST(s) were mapped for retro_mmus_2288 retrocopy.

TSS

No TSS is located nearby retro_mmus_2288 retrocopy 5' end.

Lab

retro_mmus_2288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2288 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024811	1 retrocopy	retro_cpor_1163,
Dasypus novemcinctus	ENSDNOG00000005703	2 retrocopies	retro_dnov_1591, retro_dnov_2683,
Mus musculus	ENSMUSG00000064326	1 retrocopy	retro_mmus_2288 ,
Otolemur garnettii	ENSOGAG00000016881	1 retrocopy	retro_ogar_3280,