RetrogeneDB ID: retro_ptro_2763

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:71238085..71238770(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM213A
• Ensembl ID: ENSPTRG00000002685
• Aliases: None
• Description: family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]

Sequence

>retro_ptro_2763
ATGTCTTTCTTCCAGAACCCAAGTTTCCTCACCATGGGCATGTGGTCCCTCGGTGCAGGAGCCCTGGGGGCTGCTGCCTT
GGCATTATTGCTGGCCAACACAGACATGTTTCTGTCTAAGCCCCAGAAAGCGGCACTGGAGTACCTGGAGGATATAGACC
TGAAAATGCTGGAGAAGGAACCAAGGACTTTGAAAGCAAAGGAGCTATGGGAAAAGAAAATGGACCTGTGATTATGGCTG
TGCGGAGGCCAGGCTGTTTCCTCTGTTGAGGGGAAGCTGCGGATCTGTCCTCCCTGAAACCCATGTGGACGAGCTGGGTG
TCCCCCTCTATGCAGTGGTAAAGGAGCACATCAGGACTGAAGTGAAGGATTTCCAGCCTTATTTTAAAAAAGAAACCTTC
CTGGGTGAAAAGAAAAAGTTCTATGGTCCACAAAGGCAGAAGATGATGTTTATGGGATTTATCTGTCTGGGAGTGTGGTA
CTTCTGAGCCTGGAATGGAGGCTTCTCTGGAAACCTGGAAGGAGAAGTCTTCATCCTCAGGGAAGTTTTCGTGGTGGCAT
CAGGAAACCAGGGGATTCTTCTCGAGCACCGAGAAAAAGAATTTGGAGACAAAGTAAACCTACTTTGTCTGGTTCTGGAG
GCTGCTAAGATGATCAAACCACAGACTTTGGCCTCAGAGAAAAAA

Alignment

ORF - retro_ptro_2763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFLQDPSFFTMGMWSIGAGALGAAALALLLANTDVFLSKPQKAALEYLEDIDLKTLEKEPRT-FKAK-E
          MSF.Q.PSF.TMGMWS.GAGALGAAALALLLANTD.FLSKPQKAALEYLEDIDLK.LEKEPRT.F..K..
Retrocopy MSFFQNPSFLTMGMWSLGAGALGAAALALLLANTDMFLSKPQKAALEYLEDIDLKMLEKEPRT<FESKGA

Parental  LWEKNGAVIMAVRRPGCFLCREEAADLSSLK-STLDQLGVPLYAVVKEHIRTEVKDFQPYFKGEIFLDEK
          ....NG.VIMAVRRPGCFLC..EAADLSSLK....D.LGVPLYAVVKEHIRTEVKDFQPYFK.E.FL.EK
Retrocopy MGKENGPVIMAVRRPGCFLC*GEAADLSSLK<THVDELGVPLYAVVKEHIRTEVKDFQPYFKKETFLGEK

Parental  KKFYGPQRRKMMFMGFIRLGVWYNFFRAWNGGFSGNLEGEGFILGGVFVVGSGKQGILLEHREKEFGDKV
          KKFYGPQR.KMMFMGFI.LGVWY..F.AWNGGFSGNLEGE.FIL..VFVV.SG.QGILLEHREKEFGDKV
Retrocopy KKFYGPQRQKMMFMGFICLGVWY--F*AWNGGFSGNLEGEVFILREVFVVASGNQGILLEHREKEFGDKV

Parental  NLLS-VLEAAKMIKPQTLASEKK
          NLL..VLEAAKMIKPQTLASEKK
Retrocopy NLLCLVLEAAKMIKPQTLASEKK

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	0.07 RPM	83.17 RPM
SRP007412_cerebellum	0.00 RPM	36.64 RPM
SRP007412_heart	0.00 RPM	39.67 RPM
SRP007412_kidney	0.03 RPM	76.34 RPM
SRP007412_liver	0.00 RPM	111.59 RPM
SRP007412_testis	0.11 RPM	33.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2763 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2763 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4076
Gorilla gorilla	retro_ggor_2733
Pongo abelii	retro_pabe_3345
Macaca mulatta	retro_mmul_2351

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763 , retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,