RetrogeneDB ID: retro_ptro_91

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:120877252..120877705(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005528
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSPTRG00000009415
• Aliases: None
• Description: Pan troglodytes NME/NM23 nucleoside diphosphate kinase 1 (NME1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001204512]

Sequence

>retro_ptro_91
GCCAACCTCGAGCGCACCTTCATCACCATCAGGCCGGACAGCATGCAGTGCGGCCTGGTGGGCAAGATCATCAAGCGCTT
CGAGCAGAAGGGGTTCCGCCTCGTGGCCATGAAGTTCCTCCCGGCCTCTGAAGAACACCTGAAGCAGCACTACATTGACC
TGAAGGACCGCCCAGTCTTCCCTGGGCTGGTGAAGTACATGACCTCAGGGCCGGTCGTGGCCATGGTCTGGGAGGGGCTG
AACGTCGTGAAGACAGGCCGAGTGATGCTTGGGGAGACCAATCCAGCAGATTCTAAGCCAGGCACCATTCGTGGGGACTT
TTGCATTCAGGTTGGCAGGAACATCATTCATGGCAGTGATTCAGTAAAAACTGCTGAAAAAGAAATCAGCCTACGGTTTA
AGCCTGAAGAACTGGTTGACTACAAGTCTTGTGCTCATGACTGGGTCTATGAA

Alignment

ORF - retro_ptro_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANCERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDLLKEHYVDLKDRPFFAGLVKYMHSG
          AN.ERTFI.I.PD..Q.GLVG.IIKRFEQKGFRLV..KF..ASE..LK.HY.DLKDRP.F.GLVKYM.SG
Retrocopy ANLERTFITIRPDSMQCGLVGKIIKRFEQKGFRLVAMKFLPASEEHLKQHYIDLKDRPVFPGLVKYMTSG

Parental  PVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIGLWFHPEELVD
          PVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSV..AEKEI.L.F.PEELVD
Retrocopy PVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKTAEKEISLRFKPEELVD

Parental  YMSCAQNWIYE
          Y.SCA..W.YE
Retrocopy YKSCAHDWVYE

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	18.86 RPM	63.54 RPM
SRP007412_cerebellum	14.38 RPM	44.74 RPM
SRP007412_heart	21.57 RPM	9.44 RPM
SRP007412_kidney	39.02 RPM	20.53 RPM
SRP007412_liver	51.43 RPM	43.18 RPM
SRP007412_testis	2.63 RPM	17.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_91 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_91 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_91 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1063
Gorilla gorilla	retro_ggor_71
Pongo abelii	retro_pabe_102

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91 ,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,