RetrogeneDB ID: retro_mmul_1340

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:73271223..73271679(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000014854
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: INO80C
• Ensembl ID: ENSMMUG00000020108
• Aliases: None
• Description: INO80 complex subunit C [Source:RefSeq peptide;Acc:NP_001253431]

Sequence

>retro_mmul_1340
GCCAGTAAGAAGAAAGCAGCGTCCGCCTCCAGCTCTGTGCAGGGTATCAGCGTGGAAGCCAGGAGTGAGAATAAAGTGGT
GCCGTCTGAGTTTAGCACAGGACCTGTGGAAAAAGCTGCCAAACCTTTGCCATTTAAGGATCCCAACTTTGTGCACTCTG
GCCACGGTGGCGCAGCAGCTGCCAAGAACACGACCTGGAAGAACCTGAAACAAATCCTCGCTTCCCAAAGGGCACTGCCG
TGGCAACCGAACGATCCCAACTACTTCAGTACTGATGCTCCTCCACCCTTTAAGCCAGCTAAGAAGAATTCTGATGTTCC
GGGTCTGCCTGCCAACCACAGACCCCCGAGCAAACTGCGGCTCGGCACCGTTGAAGAGTTTTCCTACATTCGGAGGCTGC
CCTCTGAGGTCACCACCGGCCACCTGGCCCTGAGGAAGGCCTCGAGCATCCTTCCC

Alignment

ORF - retro_mmul_1340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 80.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASKKKKVSASSFAQGISMEAMNENKVVPSEFSTGPVEKAAKPLPFKDPNFVHSGHGGAVAGKKNRTWKNL
          ASKKK..SASS..QGIS.EA..ENKVVPSEFSTGPVEKAAKPLPFKDPNFVHSGHGGA.A..KN.TWKNL
Retrocopy ASKKKAASASSSVQGISVEARSENKVVPSEFSTGPVEKAAKPLPFKDPNFVHSGHGGAAAA-KNTTWKNL

Parental  KQILASERALPWQLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLRFSTIEEFSYIRRLPSDVV
          KQILAS.RALPWQ.NDPNYFS.DAPP.FKPAKK.SDV.GL.AN...P.SKLR..T.EEFSYIRRLPS.V.
Retrocopy KQILASQRALPWQPNDPNYFSTDAPPPFKPAKKNSDVPGLPANHR-PPSKLRLGTVEEFSYIRRLPSEVT

Parental  TGYLALRKATSIVP
          TG.LALRKA.SI.P
Retrocopy TGHLALRKASSILP

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	0.22 RPM	8.63 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.38 RPM
SRP007412_cerebellum	0.32 RPM	11.30 RPM
SRP007412_heart	0.00 RPM	9.25 RPM
SRP007412_kidney	0.00 RPM	3.05 RPM
SRP007412_liver	0.04 RPM	2.57 RPM
SRP007412_testis	3.73 RPM	2.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1340 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017884	1 retrocopy	retro_cfam_371,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Macaca mulatta	ENSMMUG00000020108	1 retrocopy	retro_mmul_1340 ,
Ochotona princeps	ENSOPRG00000011443	1 retrocopy	retro_opri_721,
Pteropus vampyrus	ENSPVAG00000017436	1 retrocopy	retro_pvam_899,