RetrogeneDB ID: retro_pabe_1939

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:34484807..34485840(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459G1612
• Ensembl ID: ENSPPYG00000005352
• Aliases: None
• Description: succinyl-CoA ligase [Source:RefSeq peptide;Acc:NP_001124678]

Sequence

>retro_pabe_1939
CAGACCATAGTACAGTCTACTGCCCAGGTTCTGGGAATTTCTGAGCTGTTTAATAACCAATAACTCCAAGTACAGCAGCA
ACAGCAAAAGAATCTCTCACTACATGAATATATGAATATGAAATTGTTGCAAGAAGCTGGTGTCTCCCTTCCAAAGGATA
TGTGGCAAAGTCACCAGATGAAGCTGACGTAATTGTCAAAAAATTAGGTTCTAAAGATGTTGTGATAATGGCACAGAATT
TTGCTTGTGGTAGAGAAAAAGGAACATTTGAAAGCAGTCCCAAAAGAGAAGTGAAGATAGTTTTCTGTCAAGAAGCAAAA
GCTGTTTCCTCTCAAATTATCGGGAAAAAGTTGTTTACCAAGTAAACAGGAGAAAAGGACAAAATATGCAATCAAGTATT
GATCTGTGAGCAAAAATATCCCAGGAGAGAATACTACTTTCCAGTAACAATGGAAAGGTCATTTCAAGGTCCAGTATAAA
TAGGAAGTTTGCAAGGTGGTGTCAACCCTGAAGATGTTTCTGCTGAGACTCCTGATGTAATAAAGAATCTATTGATGTCG
TAGAAGGCATCAAAAAGGAACAAGCTCTCCAGCTTGCACAGAATATAAGATTTCCATCTACTATTGTGGATTCTGTGGCA
GAAAACATGGTCAAGCTTTACAATCTTTTTCTGAACTACAACACAACCATGATAAAAATAAGCTCAACAGTATAAGATTC
AGATGGAGCTCTGCTATGTTTGGACACAAAGATCAATTTTGATTCTAATTCAGTCTATCGCCAGAAGATCTTTGATCTAC
AGGACTGGGCTCAGGAAGATGAAAGGAACAAAGATGAAGCTAAGCCACATCTCAATAACATTGGCCTCAGTGGAAAAATA
GGCTGTCTAGTAAATGGTGCTGGTTTGGCTATAACCACAATAGATATAAGAAAACTTCATAAAGAGACTCCAACCAGCTT
CCTTGTTGTTCATGTTAGTGCTATAGTCCATCAAGTAACAGAATCATTTATGCTTATCACTGCAGATAAAAAG

Alignment

ORF - retro_pabe_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.86 %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSIPK-GYVAKSPDEAYAIAKKL
          .T.....AQVLG.S.LFNN..LQVQQQQQ.NLSLHEYM.M.LLQEAGVS.PK.GYVAKSPDEA..I.KKL
Retrocopy QTIVQSTAQVLGISELFNNQ*LQVQQQQQKNLSLHEYMNMKLLQEAGVSLPK<GYVAKSPDEADVIVKKL

Parental  GSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCER
          GSKDVVI.AQ..A.GR.KGTFES..K..VKIVF...EAKAVSSQ.IGKKLFTK.TGEK..ICNQVL.CE.
Retrocopy GSKDVVIMAQNFACGREKGTFESSPKREVKIVFC-QEAKAVSSQIIGKKLFTK*TGEKDKICNQVLICEQ

Parental  KYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIK-EPIDIEEGIKKEQALHLAQKMGFP
          KYPRREYYF..TMERSFQGPV.IGS..GGVN.EDV.AETP...IK.E.ID..EGIKKEQAL.LAQ...FP
Retrocopy KYPRREYYFPVTMERSFQGPV*IGSLQGGVNPEDVSAETPD-VIK<ESIDVVEGIKKEQALQLAQNIRFP

Parental  PTIVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDE
          .TIV.S.AENMVKLY.LFL.Y..TMI.I...V.DSDGA.LC.D.KINFDSNS.YRQ.KIFDLQDW.QEDE
Retrocopy STIVDSVAENMVKLYNLFLNYNTTMIKISSTV*DSDGALLCLDTKINFDSNSVYRQ-KIFDLQDWAQEDE

Parental  RDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKK
          R.KD.AK..LN.IGL.G.IGCLVNGAGLA..T.DI.KLH..TP..FL.V...A.VHQVTE.F.LIT.DKK
Retrocopy RNKDEAKPHLNNIGLSGKIGCLVNGAGLAITTIDIRKLHKETPTSFLVVHVSAIVHQVTESFMLITADKK

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	45.34 RPM
SRP007412_cerebellum	0.00 RPM	54.48 RPM
SRP007412_heart	0.00 RPM	72.07 RPM
SRP007412_kidney	0.00 RPM	33.31 RPM
SRP007412_liver	0.00 RPM	9.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1939 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1939 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2281
Pan troglodytes	retro_ptro_1615
Gorilla gorilla	retro_ggor_1694

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939 , retro_pabe_2852,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,