RetrogeneDB ID: retro_ptro_2616

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:39269819..39270443(-)
• Located in intron of: ENSPTRG00000019120

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSPTRG00000004734
• Aliases: None
• Description: None

Sequence

>retro_ptro_2616
AAAGTGTGGGATGCTATCCCAGGAGATGAACTGATGACCCTGGCTCATAAACACATTATCAAGACTATGGATTTCATGCA
GGATAGTAATTATTTGTTAACCAGGGGACAGAATAAACTGTTAAGCATATATGACTTGAACAAACCCGAAGCAGAACCTG
AGGAAATTAGTGATCACAGCTCTGATATTAAAAAGGCCCTATGGTACAGTGAGGATAAACAGATTCTTTCTTCTGATGAC
AAAACTGTTAAGACTTTGGGATCATGCTACTACGACAGAAGTGAAATCTCTAAATTTTATTATGTTGGCTAGTAGTATGG
AATATATTCCTGAGGGAGAGATTTTGGTAATAACTTATGGCTGATCCAGTGCTTTTGACAGTACAGTAAGTTTGGAACCA
ATTAAATCCTTTCAAGCTCCTGCAACCATTAACTCTGAATCTCTTCACCTTGAGAAAGAATTTCTTGTTGCAGGTGGTGA
AGATGTTAAACTTATAAGTATGATGATAATAGTGGAGAAGAATTAGAATCCTACAAAGGACACTCTGGTCCTATTCACTG
TGTGAGATTTGATCCTGATGGAGAACTCTATGCCAGTGGTTCTGAAGATGGAACACTGAGACTG

Alignment

ORF - retro_ptro_2616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 59.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEISGHTSGIKKALWCS
          KVWDA..GDELMTLAHKHI.KT.DF.QDSNYLLT.GQ.KLL.IYDLNKPEAEP.EIS.H.S.IKKALW.S
Retrocopy KVWDAIPGDELMTLAHKHIIKTMDFMQDSNYLLTRGQNKLLSIYDLNKPEAEPEEISDHSSDIKKALWYS

Parental  EDKQILSADDKTV-RLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDPIKSFEA
          EDKQILS.DDKTV.RLWDHAT.TEVKSLNF.M..SSMEYIPEGEILVITYG.S.AF.S.VSL.PIKSF.A
Retrocopy EDKQILSSDDKTV>RLWDHATTTEVKSLNFIMLASSMEYIPEGEILVITYG*SSAFDSTVSLEPIKSFQA

Parental  PATINSASLHPEKEFLVAGGEDFKL-YKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSEDGTLRL
          PATINS.SLH.EKEFLVAGGED.KL.YKYD.NSGEELESYKGH.GPIHCVRF.PDGELYASGSEDGTLRL
Retrocopy PATINSESLHLEKEFLVAGGEDVKL<YKYDDNSGEELESYKGHSGPIHCVRFDPDGELYASGSEDGTLRL

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	0.55 RPM	62.63 RPM
SRP007412_cerebellum	0.39 RPM	56.03 RPM
SRP007412_heart	0.26 RPM	60.10 RPM
SRP007412_kidney	0.50 RPM	61.82 RPM
SRP007412_liver	0.52 RPM	42.06 RPM
SRP007412_testis	0.74 RPM	71.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2616 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2616 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3723
Pongo abelii	retro_pabe_3134
Macaca mulatta	retro_mmul_1695

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616 ,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,