RetrogeneDB ID: retro_ptro_1979

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:42098040..42098637(+)
• Located in intron of: ENSPTRG00000016014

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B1
• Ensembl ID: ENSPTRG00000001653
• Aliases: None
• Description: Pan troglodytes ATPase, Na+/K+ transporting, beta 1 polypeptide (ATP1B1), mRNA. [Source:RefSeq mRNA;Acc:NM_001098555]

Sequence

>retro_ptro_1979
CCACCAGGATTAACACAGATTTCTCAGATCCAGAAGACTGAAATTGCCTTTCATCCTAATGATCCCAAGCACTGTGTGGC
ATATGTGCTGAACGTAGTTAGGTTCCTGGAAAAGTACAAAGATTCAGCCCAGAAGGATGACATGATTTTTGAAAATTGTG
ACAATGTGCCCAGTGAACCCAAAGAACGAGGAGACTTTAATCAAGAATGAGGTGAGCGAAAGGTCTGCAGATTCAAGCTT
GAGTGGCTGGGAAATTGCTCTGGATTAAATGACAAAACTTACAGCTACGAAGAGGGCAAACCACATGTTATTATAAAGCT
CAAGTGAGTTCTAGGCTTCAAACCTAAGTCTCCCGAGAATGAGTCCTTGGAGACTTACCCAGTGATGAAGTATAACGCAT
CTGTGTTTCCTGTTCAGTGCACTGGCTAGCAAGATGAAGATAAGGATAAAAATAGAAATGTGGAGTATTTTGGACTGGGC
ACCTACCTTGGTTTTCCTCTGCAGAATTATCCCTACTATGGCAAACTCCTGCAGCCCAAATACCTGCAGCCCCTGCTTGC
TGTACAGTTCACCAACCTTACCATGGACACTGAAATT

Alignment

ORF - retro_ptro_1979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.42 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDVPSEPKERGDFNHER
          PPGLTQI.QIQKTEI.F.PNDPK...AYVLN.VRFLEKYKDSAQ.DDMIFE.C..VPSEPKERGDFN.E.
Retrocopy PPGLTQISQIQKTEIAFHPNDPKHCVAYVLNVVRFLEKYKDSAQKDDMIFENCDNVPSEPKERGDFNQE*

Parental  GERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVLGFKPKPPKNESLETYPVMKYNPNVLPVQC
          GERKVCRFKLEWLGNCSGLND.TY.Y.EGKP..IIKL..VLGFKPK.P.NESLETYPVMKYN..V.PVQC
Retrocopy GERKVCRFKLEWLGNCSGLNDKTYSYEEGKPHVIIKLK*VLGFKPKSPENESLETYPVMKYNASVFPVQC

Parental  TGKRDEDKDKIGNVEYFGLGNSPGFPLQYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEI
          TG..DEDKDK..NVEYFGLG...GFPLQ.YPYYGKLLQPKYLQPLLAVQFTNLTMDTEI
Retrocopy TG*QDEDKDKNRNVEYFGLGTYLGFPLQNYPYYGKLLQPKYLQPLLAVQFTNLTMDTEI

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	0.13 RPM	668.72 RPM
SRP007412_cerebellum	0.36 RPM	415.27 RPM
SRP007412_heart	0.12 RPM	278.43 RPM
SRP007412_kidney	0.24 RPM	1121.13 RPM
SRP007412_liver	0.07 RPM	87.96 RPM
SRP007412_testis	0.21 RPM	60.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1979 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1979 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2924
Gorilla gorilla	retro_ggor_2027
Callithrix jacchus	retro_cjac_2288

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288,
Homo sapiens	ENSG00000143153	1 retrocopy	retro_hsap_2924,
Gorilla gorilla	ENSGGOG00000002499	1 retrocopy	retro_ggor_2027,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979 ,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Xiphophorus maculatus	ENSXMAG00000016407	1 retrocopy	retro_xmac_22,