RetrogeneDB ID: retro_pabe_2852

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:31176681..31177968(+)
• 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_2852
CGGACCACACTGTGGGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCATGGACTCCAAGTACAGCAGCA
ACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAATTATTGCAAGAAACTGGTGTCTCTGTTCCCAAAGGAT
ATGCGGCAAAGTGACCAGATGAAGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT
TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGGAGGAGTGAAGATGGTTTTCTCTCCAGAAGAAGC
AAAAGCTGTTTCTTCACAAATGATTAGGAAACAGTCGTTTACCAAGCAAATGGGAGAAAAGGGCAGAATATGCAATCAGG
TATTGGTTTGTGAGTGAAAATATCCCAACAGAGAGTGCTACTTTGCAATAACAATGGAAAGGTCATTTCAAGGTCTTGTA
TTAATAGGAAGTTCACATAGTGGGGTCAACATTGAAGATGTTGCTGCTGAGACTCCTGAAGCAATAATTAAAGTACCTAT
TGATATTGTAGAAGGCATCAAAGAGGAATAAGTTCTCCAGCTTGCACAGAAGATGGGATTTCCATCTAATATTGTGGCTT
CAGCAGCAGAAAACATGATCAAGTTTTACAGCCTTTTTCTGAAATACGATGCAACCGTGATGGAAATAAATCCAATGGTG
GAAGATTCAGATGGAGCTGTATTGTGTATGGATGCAAAAATCAATTTTGACTCTAATTCAGCCTATCGCCAAAAGAAAAT
CTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGAACAAAGATGCTGCTAAGGCAGATCTCAACTACACTGGCCTTG
ATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGATATAATAAAACCTCATGGAGAGACT
CCAGCCAACTTCCTTGATGTTGGTGGTGGTGCTACAGTCCATCAAGTAACAGAAGCGTTTAAGCCTATCACTTCAGATAA
AAAGGTACTGGCTATTCTGGTCAACATTTGTGGAGGAATCATACACTGTGATATTATAGCAAAGGGTATAGTCATGGCAG
TAAAAGGTTTGGAAATTAAAATACCTGTTGTACAGTTACAAGGTACACGAGTTGATGATGTTAAGGCACTAAAAGCAGAC
AGTGAACTTAAAATACTTGCTTGTGATGATTTGGTGGAAGCTGCTAGAGTGGTTGTAAAGCTCTCTGAAATAGTGAAGCA
AAGCAAG

Alignment

ORF - retro_pabe_2852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 92.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSIPKGYVAKSPDEAYAIAKKLG
          RT...AAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQE.GVS.PKGY.AK.PDEAYAIAKKLG
Retrocopy RTTLWAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQETGVSVPKGYAAK*PDEAYAIAKKLG

Parental  SKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERK
          SKDVV.KAQVLAGGRGKGTFESGLKGGVK.VFSPEEAKAVSSQMI.K..FTKQ.GEKGRICNQVLVCE.K
Retrocopy SKDVVMKAQVLAGGRGKGTFESGLKGGVKMVFSPEEAKAVSSQMIRKQSFTKQMGEKGRICNQVLVCE*K

Parental  YPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALHLAQKMGFPPT
          YP.RE.YFAITMERSFQG.VLIGSSH.GVNIEDVAAETPEAIIK.PIDI.EGIK.E..L.LAQKMGFP..
Retrocopy YPNRECYFAITMERSFQGLVLIGSSHSGVNIEDVAAETPEAIIKVPIDIVEGIKEE*VLQLAQKMGFPSN

Parental  IVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERD
          IV.SAAENM.K.YSLFLKYDAT..EINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDER.
Retrocopy IVASAAENMIKFYSLFLKYDATVMEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERN

Parental  KDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKKVL
          KDAAKA.LNY.GLDG.IGCLVNGAGLAMATMDIIK.HG.TPANFLDVGGGATVHQVTEAFK.ITSDKKVL
Retrocopy KDAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKPHGETPANFLDVGGGATVHQVTEAFKPITSDKKVL

Parental  AILVNIFGGIMRCDVIAQGIVMAVKDLEIKIPVVVRLQGTRVDDAKALIADSGLKILACDDLDEAARMVV
          AILVNI.GGI..CD.IA.GIVMAVK.LEIKIP.VV.LQGTRVDD.KAL.ADS.LKILACDDL.EAAR.VV
Retrocopy AILVNICGGIIHCDIIAKGIVMAVKGLEIKIP-VVQLQGTRVDDVKALKADSELKILACDDLVEAARVVV

Parental  KLSEIVTLAK
          KLSEIV...K
Retrocopy KLSEIVKQSK

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	0.11 RPM	45.34 RPM
SRP007412_cerebellum	0.12 RPM	54.48 RPM
SRP007412_heart	0.06 RPM	72.07 RPM
SRP007412_kidney	0.00 RPM	33.31 RPM
SRP007412_liver	0.06 RPM	9.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2852 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2852 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3445
Pan troglodytes	retro_ptro_2337
Gorilla gorilla	retro_ggor_2327

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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,