RetrogeneDB ID: retro_ptro_2876

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:17717678..17718739(-)
• Located in intron of: ENSPTRG00000020791

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSPTRG00000014483
• Aliases: None
• Description: None

Sequence

>retro_ptro_2876
ATGAGGACATTGTACACGCAGAGTTTGGAGCCTCTTCCACCAAGAGGATCTGGCTTTGGAGCATCAGAAAATGAAACTGA
ATTTGCTGAAGGTGAAAGTGAAGCTAAACAGGAAATTCTTAAAAACAAAGATCTGGCTGTTCAACATGACCATTTTGATG
GGCTTGGATGGACTAAATAAAGATAATATCACCGTTTGTAAACTGGAGATGTTTTTAAGGCTAAAAATCTCATTGAGGTA
ATGTGGAATTCTCATGAAGCCCGTGAAAAATTTCTTCATCCAGGAATTTTTTAGACAAGTGAATTTTTTGAGTGATACAT
GTCAAGGTGACAATGGATTTCCAAATGGGTTAGATGTTACCTTTGAAGTAACTGAATTAAGGAAATTAATGGGCAGTTAA
AACACCATGGTTGGAAACAATGAAGGGAGTACGGTACTTGGCCTCAAACTCCCTGATCTTCTAGGTTATGCAGAAAAGGC
GACTTTTCATTTTTCCCATGGAACAAAAGACGCTTCCCACGGCCTTTCTTCAAACCACGGCCCAGAAACTTCAAAAGGAA
TTTATCTGTAAAATTACATGAAGTTACTGAACAGTTCCCTTGGAGCTCACTTCTGGAAATGACAGAAGATGATCAGCCAG
GTACAGTCTTCCCATATGAAAGACCAGCCACACCATCAACTGGAAAGGCATGTGGCGAGACCTGGGCTGCCACTTAAGGA
CAGCATCATTTGCTGTTTGAAAGTAAGGCAGACATTCACTTAAATCATGTCTTTCACATGCCATGGTCATCGATTTTCAG
AATTCTTCCATCTTACCAAGAAAATGTGTTTTGCTGAAAGTTAACCAGGAACTGACAGGCTACACTACAAGGGATATAAG
CTTCATCAAAGATTTTGAACTTCAGTTGAATAAACCACTCATATTTGATTCAGTTTTTTCAGCATTTCTCTGAGGTGGGA
TGTTGGCACCCATGGTGATAAACTGTGAGTCCTGCTGATAGTTTCACCTTGGGGGACCAACAAGTGTCCAAGGATTCGGC
ATGCACAGCACCGGAGCAGAG

Alignment

ORF - retro_ptro_2876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.85 %
• Parental protein coverage: 75.91 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MGTVHARSLEPLPSSGPDFGGLGEEAEFVEVEPEAKQEILENKDVLVQHVHFD-GL-GRTKDDVIICEI-
          M.T....SLEPLP..G..FG....E.EF.E.E.EAKQEIL.NKD..VQH.HFD.GL.G..KD....C...
Retrocopy MRTLYTQSLEPLPPRGSGFGASENETEFAEGESEAKQEILKNKDLAVQHDHFD>GLDGLNKDNITVCKL<

Parental  GDVFKAKNLIEVMRKSHEAREKLLRLGIF-RQVDVLIDTCQGDDALPNGLDVTFEVTELRRLTGSYNTMV
          GDVFKAKNLIEVM..SHEAREK.L..GIF.RQV..L.DTCQGD...PNGLDVTFEVTELR.L.GS.NTMV
Retrocopy GDVFKAKNLIEVMWNSHEAREKFLHPGIF>RQVNFLSDTCQGDNGFPNGLDVTFEVTELRKLMGS*NTMV

Parental  GNNEGSMVLGLKLPNLLGRAEKVT-FQFSYGTKETSYGLSFFKPRPGNFERNFSVNLYKVTGQFPWSSLR
          GNNEGS.VLGLKLP.LLG.AEK.T.F.F............FFKPRP.NF.RN.SV.L..VT.QFPWSSL.
Retrocopy GNNEGSTVLGLKLPDLLGYAEKAT<FSF-FPWNKRRFPRPFFKPRPRNFKRNLSVKLHEVTEQFPWSSLL

Parental  E-TDRGMSAEYSFPIWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPR
          E..DR..SA.YS.PI.KTSHT..W.G.WR.LGC..RTASFAV.K...HSLKS.LSHAMVID..NSSILPR
Retrocopy E<NDRR*SARYSLPI*KTSHTINWKGMWRDLGCHLRTASFAV*K*GRHSLKSCLSHAMVIDFQNSSILPR

Parental  RGALLKVNQELAGYTGGDVSFIKEDFELQLNKQLIFDSVFSASFWGGMLVPI-GDK-PSSIADRF-YLGG
          ...LLKVNQEL.GYT..D.SFIK.DFELQLNK.LIFDSVFSA...GGML.P..GDK...S.AD.F..LGG
Retrocopy KCVLLKVNQELTGYTTRDISFIK-DFELQLNKPLIFDSVFSAFL*GGMLAPM<GDK<TVSPADSF<HLGG

Parental  PTSVRGFSMHSIGPQ
          PTSV.GF.MHS.G..
Retrocopy PTSVQGFGMHSTGAE

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	39.32 RPM
SRP007412_cerebellum	0.00 RPM	48.29 RPM
SRP007412_heart	0.00 RPM	77.15 RPM
SRP007412_kidney	0.03 RPM	89.26 RPM
SRP007412_liver	0.00 RPM	70.02 RPM
SRP007412_testis	0.11 RPM	65.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2876 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2876 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4233
Pongo abelii	retro_pabe_3404
Macaca mulatta	retro_mmul_1152
Callithrix jacchus	retro_cjac_605

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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	ENSCJAG00000015070	2 retrocopies	retro_cjac_2277, retro_cjac_605,
Homo sapiens	ENSG00000100347	1 retrocopy	retro_hsap_4233,
Macaca mulatta	ENSMMUG00000015446	1 retrocopy	retro_mmul_1152,
Nomascus leucogenys	ENSNLEG00000015693	1 retrocopy	retro_nleu_1035,
Pongo abelii	ENSPPYG00000011918	1 retrocopy	retro_pabe_3404,
Pan troglodytes	ENSPTRG00000014483	1 retrocopy	retro_ptro_2876 ,