RetrogeneDB ID: retro_ptro_1864

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:18127607..18128473(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSPTRG00000002585
• Aliases: None
• Description: None

Sequence

>retro_ptro_1864
ATGAGCGGCTTCAGCACCGAGGTGCACACCGCACCCTTCTCCCTGTAGTACCGAGTCTTCCTCAAAAATGAGAAAGGACA
ATATATATCTCCATTTCATAATATTCCAATTTATGCAGATAAGGATGTGTTCCACGTGGTAGTTGGAAGTACCACGCTGT
CTAATGCAAAAATGGAGATTGCTACAAAGGACCCTTTAAACCCCATTAAACAAGATGTGAAAAAAGAAAAACTTCGTTAT
GTTGCGAATTTGTTCCTGTATAAAGGATATATCTGGAACTATGGTGCCATCCCTCAGACTTGGAAAGACCCAGGGCACAA
TGATGAACATACTGGCTGTTGTGGTGACAGTGACCCAATTGATGTGTGTGAAATTGGAAGCAAGGTATGTGCAAGAGGTG
AAATAATTGGCATGAAAGTTCTAGGCATATTGGCTATGATTGACAAAGGGGAAACTAACTGGAAAGTCATTGCCATCAAT
GTAGATGATCCTGATGCAGCCAATTGTAATGATACCAATGATGTCAAACAGCTGAAACCTGGCTACTTAGAAGCTACTGT
GGACTGGGTTAGAAGGTATAAGGTTCCTGATGGAAAACTAGAAATGAGTTTGCTTTTAATGCAGAATTTAAAGATAAGGA
CTTTGCAATTGATACTATTAAAACCACTCATGACCATTGGAAAGCATTAGTGACTAAGAAAATGAATGGAAAGGGAATCA
GTTGCATGAATACAACTGTGTCCAAGAGCCCCTTCAAGTGTGATCCTGATGCTGCCAGAGCCATTGTGGATGCTTTACCA
CCACCCTGTGAATCTGCCTGCACAGTACCAACAGATGTGGATAAGTGGTTCCATTACCAGAAAAAC

Alignment

ORF - retro_ptro_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGFSTEERAAPFSLEYRVFLKNEKGQYISPFHDIPIYADKDVFHMVVEVPRWSNAKMEIATKDPLNPIK
          M.GFSTE...APFSL.YRVFLKNEKGQYISPFH.IPIYADKDVFH.VV.....SNAKMEIATKDPLNPIK
Retrocopy MSGFSTEVHTAPFSL*YRVFLKNEKGQYISPFHNIPIYADKDVFHVVVGSTTLSNAKMEIATKDPLNPIK

Parental  QDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVKV
          QDVKK.KLRYVANLF.YKGYIWNYGAIPQTW.DPGHND.HTGCCGD.DPIDVCEIGSKVCARGEIIG.KV
Retrocopy QDVKKEKLRYVANLFLYKGYIWNYGAIPQTWKDPGHNDEHTGCCGDSDPIDVCEIGSKVCARGEIIGMKV

Parental  LGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPE-NEFAFNAE
          LGILAMID.GET.WKVIAINVDDPDAAN.ND.NDVK.LKPGYLEATVDW.RRYKVPDGK.E.NEFAFNAE
Retrocopy LGILAMIDKGETNWKVIAINVDDPDAANCNDTNDVKQLKPGYLEATVDWVRRYKVPDGKLE<NEFAFNAE

Parental  FKDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTVSESPFKCDPDAARAIVDALPPPCESACTVPTD
          FKDKDFAID.IK.THDHWKALVTKK.NGKGISCMNTTVS.SPFKCDPDAARAIVDALPPPCESACTVPTD
Retrocopy FKDKDFAIDTIKTTHDHWKALVTKKMNGKGISCMNTTVSKSPFKCDPDAARAIVDALPPPCESACTVPTD

Parental  VDKWFHHQKN
          VDKWFH.QKN
Retrocopy VDKWFHYQKN

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	0.09 RPM	99.35 RPM
SRP007412_cerebellum	0.04 RPM	81.09 RPM
SRP007412_heart	0.03 RPM	48.41 RPM
SRP007412_kidney	0.08 RPM	69.01 RPM
SRP007412_liver	0.03 RPM	95.45 RPM
SRP007412_testis	0.11 RPM	65.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1864 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1864 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2756
Macaca mulatta	retro_mmul_1540

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864 , retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,