RetrogeneDB ID: retro_mmul_2377

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:147564947..147566017(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016079
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRIP6
• Ensembl ID: ENSMMUG00000021252
• Aliases: None
• Description: None

Sequence

>retro_mmul_2377
TCAGGGCTCACCTGACTGCCCCTGAAGCAGCCAGAGCCCACCAGAGCCCCTCAGGGGACAGCGATCCCCTGAGGTATCCC
GGGGCCACCACCGGGCCACGGAGCAGCACTCCAGCCCCACTCCAGGGTCATTTTTTGCCCTCTCCCATCTGAGCAGTGTT
ACCAGGCCCCAGGGGGACCTGAGAATTAGGGCCGGCCTGGGTGGGGTCCCATGGAGTACTCCAGCGCACTCAGGGGCTCC
CTGCAGACGGGGGGCCTTCGCCCCGGAAGCCTGGACGCTGAGATAGACTTGCTGAGCAGCACGCTGGCCGAGCTGAAGGG
GGGTCGGGGTCATGCGCCCCTGCGACCAGACCAACAGGCAGAGCCCCGGCCACCTCCTGCCTCCCGCCCGGGCTCTCTGA
AGCCGAACCCAGCCTCGCGCTCCCAGCGTCTCCCTATGGGGCCCCACTGCAGCCTCTTATGCTGCCGCCAGCCCCCCCGG
CCGGCCTTCCCCGTGCAAGCAAAGGTGGCACAGTCAGTGAGGGGCTGCGGCCCACCCAGGCGGGGAACCTCTCAGGCCTC
TGGGCCCCTCCCGGGCCCCCACTTTCTGTCCCAGGCCAAGGTGAAGTCTGGGGGCCTGGCTATAGGAGCCAGAGAGAGCC
AGGGCCGGGGGCCAAAGAGGAAGCTGCGGGGGTCTCTGGCCCCGCAGGAGGAGGAAGAGGACGCGAGCACGGCCCCAGGT
GCCCCTGAGCCACCTCGGGAGGATGAGCTTGTCAGGCTGTCGAAGAAGCAGGTGCACGACATGAACCACCCGCCCAGCTG
GGAGTACTTTGGCCAGTGTGGTGGCTGCGGAGATGTGGTCGGGGATGGGGCTGGGGTTGTGGCCCTCGATTGCGTCTTTC
ATGTGGGCTGTTTTGTGTGTTCTACATGCCGGGCCCAGCTTCGGGGACAGCATTTCTACGCCATGGAGAGAGGGCGTGTT
GCCAGGGCTGCTACGTGGCCACCCGGGAGAAATGTGCCACGTGCTCCCAGCCCACCCTGGACCGGATCCTGCGGGCTATG
GGGAAGGACTACCACCCCAGCTGCTTCACC

Alignment

ORF - retro_mmul_2377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 76.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  SGPTWLPPKQPEPARAPQGRAIPRGTPGPPPAHGAALQPHPRVNFCPLPSEQCYQAPGGPE-DRGPAWVG
          SG.T.LP.KQPEP.RAPQG.AIP.G.PGPPP.HGAALQPH.RV.FCPLPSEQCYQAPGGPE...GPAWVG
Retrocopy SGLT*LPLKQPEPTRAPQGTAIP*GIPGPPPGHGAALQPHSRVIFCPLPSEQCYQAPGGPE<ELGPAWVG

Parental  SHGVLQRTQGL-PADRG-GLRPGSLDAEIDLLSSTLAELNGGRGHVPRRPERQAYEPLPPPAYRTGSLKP
          SHGVLQRTQGL.P..RG.GLRPGSLDAEIDLLSSTLAEL.GGRGH.P.RP..QA.EP.PPPA.R.GSLKP
Retrocopy SHGVLQRTQGL<PCRRG<GLRPGSLDAEIDLLSSTLAELKGGRGHAPLRPDQQA-EPRPPPASRPGSLKP

Parental  NPAS-PLPASPYG-GPTPASYATASTPAG-PAFPVQVKVAQPVRGCGPPRRGASQASGPLPGPHF-PLPG
          NPAS..LPASPYG.GPT.ASYA.AS.P.G.PAFPVQ.KVAQ.VRGCGPPRRG.SQASGPLPGPHF...PG
Retrocopy NPAS<ALPASPYG<GPTAASYAAAS-PPG<PAFPVQAKVAQSVRGCGPPRRGTSQASGPLPGPHF<SVPG

Parental  RGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGGEHG-PQVHLSQ-PPEDELDRLTKKLVHDMNHPPS
          .GEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRG.EHG.PQV.LS..P.EDEL.RL.KK.VHDMNHPPS
Retrocopy QGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGREHG<PQVPLSH<PREDELVRLSKKQVHDMNHPPS

Parental  GEYFGQCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVER-RAYCEGCYVATLEKCAT
          .EYFGQCGGCG.DVVGDGAGVVALD.VFHVGCFVCSTCRAQLRGQHFYA.ER.RA.C.GCYVAT.EKCAT
Retrocopy WEYFGQCGGCG-DVVGDGAGVVALDCVFHVGCFVCSTCRAQLRGQHFYAMER<RACCQGCYVATREKCAT

Parental  CSQPILDRILRAMGKAYHPGCFT
          CSQP.LDRILRAMGK.YHP.CFT
Retrocopy CSQPTLDRILRAMGKDYHPSCFT

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	0.00 RPM	2.69 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	7.70 RPM
SRP007412_cerebellum	0.00 RPM	4.84 RPM
SRP007412_heart	0.00 RPM	11.07 RPM
SRP007412_kidney	0.00 RPM	10.45 RPM
SRP007412_liver	0.00 RPM	2.38 RPM
SRP007412_testis	0.04 RPM	7.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2377 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2377 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024772	1 retrocopy	retro_btau_1521,
Macaca mulatta	ENSMMUG00000021252	1 retrocopy	retro_mmul_2377 ,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,