RetrogeneDB ID: retro_pabe_2934

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:7561784..7562879(-)
• Located in intron of: ENSPPYG00000016206

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSPPYG00000003340
• Aliases: None
• Description: 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]

Sequence

>retro_pabe_2934
ATGAGTCATCAGTCAGACACCCTTCCTGTGCCGTCTGGCCAGATGAGAGGCCAGGTCCTCAGATACCAGAGCATCTATAC
CCAGCTGTTGAGATGATGCTGCACTTGCGGCAGACCATGAGGGAGTACTTCGTGCAGCTGGTGAGCAGGCAGGGCCTGCC
GCTGGAAGAATGGAGGCACACTCAGGCCATCCGTGAGCATGAAGCCCTTCTGGGTCGCTTAATGTGCCAGATGATCCAGC
TCCTATAGTCTGGGACCATAAGTGGCCTGGAGCTCCAAGTGCCTCTTCCTTCCCAGGACTCTAGGGGTGATGTCAGATAT
GGGCAGGGGGCCCAACTGTCCAGGCAGCCTGATCCAGTTCCCCAACTGAGTGATTGTGAAGCTGCCTTCATCAGCCGTGA
CCTATCCAACTGTGGGATTGACATCTCTGTCTTCTATTAGTCGAGCTTCCAGGACTACAATGCCTACCAAAAAGACAAAT
AGCATAAGGACAAGAACACCTTGAGCTTCGTTAACCTTGGCACCAGTGAGAACAAGCTGTGCATAGATCTGATGACTGAA
AGATTGAAAGAAAGTGACATGAACTGCATTGAGGACATCTTGCTGCAGTACCCTGATTGGAGAGGGCACCCGTTCCTGCA
AGAAGAAGTGGCCCAGTTCCTGACCTACTAGTGCAAGGCACCTGCCCGACTTGATCCAGAAAATGTGGTTGTTCTAAATG
GCTGCTGCTCTGTCTTCTCTGCACTGGCCATGGTTCTGTGTGATCCAGGCAAGGCCTTCCTGGTCCCTGCTCCCTTCTAT
AGTGGCTTTGACTTTAGCTCCTGCCTGTATGTGAAGGTTGAGTTGATTCCTGTCCACCTGGAGAGTGAGATCACTGTTAC
AAACACCCATCCTTTCCACCTCACTATGGACAAGTTAGAGGAAGCCCTGCTTGAAGCTAGGCTTGAGGGGAAAAAGGTCC
GAGGCCTTGTGCTAATCAACCCTCAGAATCTTCTGGGTGACATCTACTCCTCAGACTCGCGATGGAATACCTGGAATTTG
CCAAGAGGTATAACCTACATGTGATCATAGTGAGATTTACATGCTGTCTGTGTTT

Alignment

ORF - retro_pabe_2934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.93 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHRSDTLPVPSGQRRGQVPRDHSIYIQLL-EITLHLQQAMTEHFVQLTSRQGLSLEERRHTEAICEHEA
          MSH.SDTLPVPSGQ.RGQV.R..SIY.QLL.E..LHL.Q.M.E.FVQL.SRQGL.LEE.RHT.AI.EHEA
Retrocopy MSHQSDTLPVPSGQMRGQVLRYQSIYTQLL<EMMLHLRQTMREYFVQLVSRQGLPLEEWRHTQAIREHEA

Parental  LLSRLICRMINLLQSGATSGLELQVPLPSEDSRGDVRYGQRAQLSGQPDPVPQLSDCEPAFVSRDLSNRG
          LL.RL.C.MI.LL.SG..SGLELQVPLPS.DSRGDVRYGQ.AQLS.QPDPVPQLSDCE.AF.SRDLSN.G
Retrocopy LLGRLMCQMIQLL*SGTISGLELQVPLPSQDSRGDVRYGQGAQLSRQPDPVPQLSDCEAAFISRDLSNCG

Parental  IDISVFYQSSFQDYNAYQKDKYHKDKNTLGFINLGTSENKLCMDLMTERLQQSDMNCIEDTLLQYPDWRG
          IDISVFY.SSFQDYNAYQKDK.HKDKNTL.F.NLGTSENKLC.DLMTERL..SDMNCIED.LLQYPDWRG
Retrocopy IDISVFY*SSFQDYNAYQKDK*HKDKNTLSFVNLGTSENKLCIDLMTERLKESDMNCIEDILLQYPDWRG

Parental  QPFLREEVARFLTYYCRAPTQLDPENVVVLNGYCSVFSALAMVLCDPGEGFLVPAPFYGGFAFSSRLYAK
          .PFL.EEVA.FLTY.C.AP..LDPENVVVLNG.CSVFSALAMVLCDPG..FLVPAPFY.GF.FSS.LY.K
Retrocopy HPFLQEEVAQFLTY*CKAPARLDPENVVVLNGCCSVFSALAMVLCDPGKAFLVPAPFYSGFDFSSCLYVK

Parental  VELIPVHLESEVTVTNTHPFQLTVDKLEEALLEARLEGKKVRGLVLINPQNPLGDIYSPDS-LMKYLEFA
          VELIPVHLESE.TVTNTHPF.LT.DKLEEALLEARLEGKKVRGLVLINPQN.LGDIYS.DS..M.YLEFA
Retrocopy VELIPVHLESEITVTNTHPFHLTMDKLEEALLEARLEGKKVRGLVLINPQNLLGDIYSSDS<AMEYLEFA

Parental  KRYNLHVII-DEIYMLSVF
          KRYNLHVII..EIYMLSVF
Retrocopy KRYNLHVII<SEIYMLSVF

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	0.00 RPM
SRP007412_cerebellum	0.12 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.03 RPM
SRP007412_kidney	0.07 RPM	0.00 RPM
SRP007412_liver	0.24 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2934 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2934 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3553
Pan troglodytes	retro_ptro_2414

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934 ,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,