RetrogeneDB ID: retro_ptro_2731

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:17081980..17082485(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM220
• Ensembl ID: ENSPTRG00000008909
• Aliases: None
• Description: Pan troglodytes transmembrane protein 97 (TMEM97), mRNA. [Source:RefSeq mRNA;Acc:NM_001251914]

Sequence

>retro_ptro_2731
TGCATGGAGTGGCTGCTGGGCCTCTACTTCCTCAGCCACAACCCCATCACCCTGTTCATGGACCTGTAGGCGGTGCTGCC
GTGTGAGCTCTACCCAGTAGAGTTTAGAAATCTGCTGAAGTGCTATGCTAAGGAGTTCAAAGGCCCGCTGCTACAGGAGC
CACCAGTTTGGTTTAAGTCCTTTCTGTTTTGCGAGCTTGTATTTCAGGTGCCTTTCTTTCCCATTGCAACCTATGCCTTC
CTCAAAGGAAGCTGCAAGTGGATTCGAACCCCTGCAAATCATCTACTCAGTTCACACCATGATGACTTTAATTCCACTAC
TCTCCACATTTCTGTTGGAGGATTTCTCCAAAGCCAGTGGTTTCAAAGGATAAAGACCTGAGACTCTGCATGAACGGTTA
ACCCCTGTATCTGTCTATGCCCCCTACTTACTCATCCCATTCGTACTTTTAATTTTCATGTTGCAGAGCCCCTACTACAA
GTATGAGGAGAAAAGAAAAAAGAAA

Alignment

ORF - retro_ptro_2731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 95.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVEWLLGLYFLSHIPITLFVDLQAVLPRELYPVEFRNLLKWYAKEFKDPLLQEPPAWFKSFLFCELVFQL
          C.EWLLGLYFLSH.PITLF.DL.AVLP.ELYPVEFRNLLK.YAKEFK.PLLQEPP.WFKSFLFCELVFQ.
Retrocopy CMEWLLGLYFLSHNPITLFMDL*AVLPCELYPVEFRNLLKCYAKEFKGPLLQEPPVWFKSFLFCELVFQV

Parental  PFFPIATYAFLKGSCKWIRTPA-IIYSVHTMTTLIPILSTFLFEDFSKASGFKGQRPETLHERLTLVSVY
          PFFPIATYAFLKGSCKWIRTPA.IIYSVHTM.TLIP.LSTFL.EDFSKASGFKG.RPETLHERLT.VSVY
Retrocopy PFFPIATYAFLKGSCKWIRTPA>IIYSVHTMMTLIPLLSTFLLEDFSKASGFKG*RPETLHERLTPVSVY

Parental  APYLLIPFVLLIFMLRSP-YKYEEKRKKK
          APYLLIPFVLLIFML.SP.YKYEEKRKKK
Retrocopy APYLLIPFVLLIFMLQSPYYKYEEKRKKK

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	4.50 RPM
SRP007412_cerebellum	0.00 RPM	5.56 RPM
SRP007412_heart	0.00 RPM	1.63 RPM
SRP007412_kidney	0.00 RPM	2.93 RPM
SRP007412_liver	0.00 RPM	23.47 RPM
SRP007412_testis	0.00 RPM	14.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2731 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2731 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4027
Gorilla gorilla	retro_ggor_2703
Pongo abelii	retro_pabe_3307
Macaca mulatta	retro_mmul_2323

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731 ,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,