RetrogeneDB ID: retro_pabe_3404

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:44775271..44776441(+)
• Located in intron of: ENSPPYG00000019201

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSPPYG00000011918
• Aliases: None
• Description: sorting and assembly machinery component 50 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24276]

Sequence

>retro_pabe_3404
ATGAGGACATTGTACACGCAGAGTTTGGAGCCTCTTCCACCAAGAGGATCTGGCTTTGGAGCATCAGAAAAATGAAACTG
AATTTGCTGAAGGTGAAAGTGAAGCTAAACAGGAAATTCTTAAAAACAAAGATTTGGCTGTTCAACATGCCCATTTCGAT
GGGCTTGGATGGACTAAATAAAGATAATATCACCGTTTGTAAAACTGGAGATGTTTTTAAGGCTAAAAACCTCACTGAGG
TAATGTGGAACTCTCATGAAGCCCGTGAAAAATTTCTTCATCCAGGAATTTTTTAGACAAGTGGATTTTTTGAGTGATAC
ATGTCAAGGTGACAATGCATTTCCAAATGGGTTAGATGTTACCCTTGAAGTAACTGAATTAAAGAAATTAATGGGCAGTT
AAAACACCATGGTTGGAAACAATGAAGGGAGTATGGTACTCGGCCTCAAACTCCCTAATCTTCTAGGTTATGCAGAAAAG
GTGACTTTTAATTTTTCCCATGGAACAAAAGAAGCTTCTCATGGCCTTTCTTCAAAACATGGCCCAGAAACTTCAAAAGG
AATTTATCTGTAAACTTACATAAAGTTACTGAACAGTTCCCTTGGAGCTCACTTCCGGAGATGAACAGAAGATGATCAGC
CAAGTACAGTCTTCCCATATGAAAGACCAGCAACACCATCAATTGGAAAGGCATGTGGTGAGACCTGGGCTGCCACTTAA
GGACAGCATCATTTGCTGTTTGAAAGTAAGGCAGACATTCACTTAAATCATCTCTTTCACATGCCATGGTCATCGATTTT
CAGAATTCTTCCATCTTACCAAGAAAATGTGTTTTGCTGAAAGTTAACCAGGAACGGACAGGCTACACTACAAGGGATAT
AAGCTTCATCAAAGATTTTGAACTTCAGTTGAATAAACCACTCATATTTGATTCAGTTTTTTCAGCATTTCTCTGAGGTG
GGATGTTGGCACCCATGGTGATAAACTATGAGTCCTGCTGATAGTTTCACCTTGGGAGACCAACAAGTGCCCAAGGATTC
AGCATGCATAGCACCGGAGCAAAGTGCAGGCGACCACCTAGGTGGAGAAGCACGCTGGGCCAGCAGCCTGCATCTGTATA
CCCCAGCACGTTTACAGCCAAACCAGGGCAGTTTGGGAGAACTTTTCCAA

Alignment

ORF - retro_pabe_3404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 83.58 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGTVHARSLEPLPSSGPDFGGLGE-EAEFVEVEPEAKQEILENKDVVVQHVHFD-GL-GRTKDDIIICEI
          M.T....SLEPLP..G..FG.....E.EF.E.E.EAKQEIL.NKD..VQH.HFD.GL.G..KD.I..C..
Retrocopy MRTLYTQSLEPLPPRGSGFGASEK>ETEFAEGESEAKQEILKNKDLAVQHAHFD>GLDGLNKDNITVCKT

Parental  GDVFKAKNLIEVMRKSHEAREKLLRLGIF-RQVDILIDTCQGDDALPNGLDVTFEVTELRRLTGSYNTMV
          GDVFKAKNL.EVM..SHEAREK.L..GIF.RQVD.L.DTCQGD.A.PNGLDVT.EVTEL..L.GS.NTMV
Retrocopy GDVFKAKNLTEVMWNSHEAREKFLHPGIF>RQVDFLSDTCQGDNAFPNGLDVTLEVTELKKLMGS*NTMV

Parental  GNNEGSMVLGLKLPNLLGRAE-KVTFQFSYGTKETSYGLSFFKPRPGNFERNFSVNLYKVTGQFPWSSLR
          GNNEGSMVLGLKLPNLLG.AE.K..F.F.......S....FFK..P.NF.RN.SVNL.KVT.QFPWSSL.
Retrocopy GNNEGSMVLGLKLPNLLGYAE<KGDF*F-FPWNKRSFSWPFFKTWPRNFKRNLSVNLHKVTEQFPWSSLP

Parental  ETDRGMSAEYSFPIWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPRR
          E..R..SA.YS.PI.KTS.T..W.G.W..LGC..RTASFAV.K...HSLKSSLSHAMVID..NSSILPR.
Retrocopy EMNRR*SAKYSLPI*KTSNTINWKGMW*DLGCHLRTASFAV*K*GRHSLKSSLSHAMVIDFQNSSILPRK

Parental  GALLKVNQELAGYTGGDVSFIKEDFELQLNKQLIFDSVFSASLWGGMLVPI-GDK-PSSIADRFYLGGPT
          ..LLKVNQE..GYT..D.SFIK.DFELQLNK.LIFDSVFSA.L.GGML.P..GDK...S.AD.F.L.G..
Retrocopy CVLLKVNQERTGYTTRDISFIK-DFELQLNKPLIFDSVFSAFL*GGMLAPM<GDK<TMSPADSFTL-GDQ

Parental  SVRGFSMHSIGPQSEGDYLGGEAYWAGGLHLYTPLPFRPGQGGFGELFR
          .V...S......QS.GD.LGGEA.WA..LHLYTP....P.QG..GELF.
Retrocopy QVPKDSACIAPEQSAGDHLGGEARWASSLHLYTPARLQPNQGSLGELFQ

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	0.06 RPM	42.91 RPM
SRP007412_cerebellum	0.49 RPM	36.97 RPM
SRP007412_heart	0.03 RPM	44.22 RPM
SRP007412_kidney	0.13 RPM	61.65 RPM
SRP007412_liver	0.40 RPM	27.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3404 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3404 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4233
Pan troglodytes	retro_ptro_2876
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,