RetrogeneDB ID: retro_ptro_1997

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:73670263..73670758(+)
• Located in intron of: ENSPTRG00000016078

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSPTRG00000017453
• Aliases: None
• Description: None

Sequence

>retro_ptro_1997
GGTCTCCTTCATCTCAGCATTTTACCCCAATCCCAGGTCCACACAAGTGCTTCTCTTGACACTTCTCAAAAATGGGAGAA
GAAGAATAAAACCGTTTATCCTCCACAACTGCCTGCAGAACCTCAGAGACCAGCAGAAATCTACCAATACCAAAGAAAAC
TAAAAGACAGCAAAGACAAGATGTTGTATTTGGCAAAATTGGTAGGAGAAATGTCCACTGACCAGGCTTAGCTCAATTGG
GATTCAGTGACAAAAAGGGACCCAAATCATTAAAGATGTTCTCTTAGAAGCACAAGACGTGGCAGTGAAAGACCACAATG
TGGAATTCAGATCTGGTTTATATATAAACTGAGTCCACCTCAGGGGGAGGCCAGTGCCTGACAGGCTTCTGCTACCAAAG
TAGAGGTTGCTTTGGGATCATGAAGGTTACTGCCATTATTTTATGAAGCTGGTGGAAGGGCCTCCCCACCTCCATGTGAG
GCACCCAAGATGGCG

Alignment

ORF - retro_ptro_1997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.09 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKLALGVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLIRG
          G.L.L..LPQS..HTSASLD.S.KWEKKNK.VYPPQLP.EP.RPAEIY...R..K.SKDKM.YLAKL...
Retrocopy GLLHLSILPQSQVHTSASLDTSQKWEKKNKTVYPPQLPAEPQRPAEIYQYQRKLKDSKDKMLYLAKLVGE

Parental  MSIDQA-LAQLEFNDKKGAK-IIKEVLLEAQDMAVRDHNVEFRSNLYI-AESTSGRGQCLKRIRYHGRGR
          MS.DQA.LAQL.F.DKKG.K.IIK.VLLEAQD.AV.DHNVEFRS.LYI..ESTSG.GQCL....Y..RG.
Retrocopy MSTDQA<LAQLGFSDKKGPK<IIKDVLLEAQDVAVKDHNVEFRSGLYI>TESTSGGGQCLTGFCYQSRGC

Parental  FGIMEKV-YCHYFVKLVEGPP-PPP-EPPKTA
          FGIM.KV.YCHYF.KLVEGPP.PPP.E.PK.A
Retrocopy FGIM-KV<YCHYFMKLVEGPP<PPPCEAPKMA

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	16.53 RPM
SRP007412_cerebellum	0.00 RPM	21.08 RPM
SRP007412_heart	0.00 RPM	27.16 RPM
SRP007412_kidney	0.00 RPM	24.63 RPM
SRP007412_liver	0.00 RPM	28.90 RPM
SRP007412_testis	0.11 RPM	46.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1997 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1997 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3041
Gorilla gorilla	retro_ggor_2095
Pongo abelii	retro_pabe_2436
Macaca mulatta	retro_mmul_1889
Callithrix jacchus	retro_cjac_2187

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Callithrix jacchus	ENSCJAG00000007325	2 retrocopies	retro_cjac_2187, retro_cjac_2558,
Homo sapiens	ENSG00000082515	1 retrocopy	retro_hsap_3041,
Gorilla gorilla	ENSGGOG00000010232	1 retrocopy	retro_ggor_2095,
Mus musculus	ENSMUSG00000020514	1 retrocopy	retro_mmus_1294,
Nomascus leucogenys	ENSNLEG00000016692	1 retrocopy	retro_nleu_1928,
Pongo abelii	ENSPPYG00000015979	1 retrocopy	retro_pabe_2436,
Pan troglodytes	ENSPTRG00000017453	1 retrocopy	retro_ptro_1997 ,