RetrogeneDB ID: retro_ptro_680

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:30269383..30270117(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: METTL15
• Ensembl ID: ENSPTRG00000003461
• Aliases: METTL15, METT5D1
• Description: None

Sequence

>retro_ptro_680
ATGCTTCAGTATCCTTATTTTTGTAGAATGTATAAAGAATGTCTTTCATGTTGGTTGGAATCTGGCATACCTAATTTAGG
TATCTGGCCAAAAAGAATACATACTACAGCAGAAAAATATGAAGAATATGAAGCCCAGAAGCAAACAGACCAAACTCAAG
CCCAGGAGTTACGCAGATCTCAAGGTAGAGATTTTGAAACTATGGCTAAATTACATACTCCAGTAACGGTGGATGAAGTT
GTTCATTGTTTGTCACCACAAAAAGGACAGATTTTTTCTAGATATGACATTTGGTTCGGGAGGGCACACAAAAGCCATTC
TACAGAAGGAGTCAGATATTGTTCTGTATGCCTTGGACACAAACCCGACAGCTTATGCATTAGCTGAACATCTTTCAGAG
TTGTATCCTAAACAAATCCGAGCTATGCTGGGCCAGTTCAGCCAGGCAGAAGCCTTGTTAATGAAAGCTGGAGTGCAGCC
AGGGACTTTTGATGGAGTTCTTATGGATCTTGGGTGTTCCTCCATGCAACTCGATACTCCTGAAAGATTTTTCCCTTTGG
AAAGACGGCCCCTTGGACATGAGGATGGATGGTAGCAGATACCCTGACATGCCCACTGCTGCTGATGTTGTGAATGCTTT
AGATCAACAGGCACTTGCATCTATCCTGAGAACATACGGGGAGGAGAAGCATGCCAAGAAAATCGCTTCAGCAATTGTTC
AGGCACGCAGCATC

Alignment

ORF - retro_ptro_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 60.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLRYPYFCRMYKECLSCWLESGKPNLGVWPKRIHTTAEKYREYEAREQTDQTQAQELHRSQDRDFETMAK
          ML.YPYFCRMYKECLSCWLESG.PNLG.WPKRIHTTAEKY.EYEA..QTDQTQAQEL.RSQ.RDFETMAK
Retrocopy MLQYPYFCRMYKECLSCWLESGIPNLGIWPKRIHTTAEKYEEYEAQKQTDQTQAQELRRSQGRDFETMAK

Parental  LHIPVMVDEVVHCLSPQKGQIF-LDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHLSELYPKQI
          LH.PV.VDEVVHCLSPQKGQIF.LDMTFGSGGHTKAILQKESDIVLYALD..PTAYALAEHLSELYPKQI
Retrocopy LHTPVTVDEVVHCLSPQKGQIF>LDMTFGSGGHTKAILQKESDIVLYALDTNPTAYALAEHLSELYPKQI

Parental  RAMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPERGFSLRKDGPL-DMRMDGGRYPDMPTAA
          RAMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPER.F.L....PL.DMRMDG.RYPDMPTAA
Retrocopy RAMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPERFFPLER-RPL>DMRMDGSRYPDMPTAA

Parental  DVVNALDQQALASILRTYGEEKHAKKIASAIVQARSI
          DVVNALDQQALASILRTYGEEKHAKKIASAIVQARSI
Retrocopy DVVNALDQQALASILRTYGEEKHAKKIASAIVQARSI

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_prefrontal_cortex	0.00 RPM	5.09 RPM
SRP007412_cerebellum	0.00 RPM	5.45 RPM
SRP007412_heart	0.00 RPM	8.31 RPM
SRP007412_kidney	0.00 RPM	8.89 RPM
SRP007412_liver	0.00 RPM	3.99 RPM
SRP007412_testis	0.00 RPM	7.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_680 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_680 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1123
Macaca mulatta	retro_mmul_870
Callithrix jacchus	retro_cjac_3301

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301, retro_cjac_4047,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680 ,