RetrogeneDB ID: retro_ptro_2414

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:7398205..7399302(-)
• Located in intron of: ENSPTRG00000017699

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSPTRG00000028662
• Aliases: None
• Description: 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like [Source:HGNC Symbol;Acc:34391]

Sequence

>retro_ptro_2414
ATGAGTCATCAGTCAGACACCCTTCCTGTGCCGTCTGGCCAGATGAGAGGCCAGGTCCTCAGAGACCAGAGCATCTATAC
CCAGCTGTTGAGATGATGCTGCACTTGCAGTAGACCATGAGGGAGTACTTCGTGCAGCTGATGAGCAGGCAGGGCCCTGC
CGCTGGAAGAATGGAGGCACACTCAGGCCGTCCGTGAGCATGAAGCCCTTCTGGGTCGCTTAATGTGCCAGATGATCCAG
CTCCTATAGTCTGGGGCCATAAGTGGCCTGGAGCTCCAAGTGCCTCTTCCTTCCCAGGACTCTAGGGGTGATGTCAGATA
TGGGCAGGGGGCCCAACTGTCCAGGCAGCCTGATCCAGTTCCCCAACTGAGTGATTGTGAAGCTGCCTTCATCAGCCGTG
ACCTATCCAACTGTGGGATTGACATCTCTGTCTTCTATTAGTCGAGCTTCCAGGACTACAATGCCTACCAAAAAGACAAA
TATCATAAGGACAAGAACACCTTGAGCTTCGTTAACCTTGGCACCAGTGAGAACAAGCTCTGCATAGATCTGATGACTGA
AAGATTGCAAGAAAGTGACACGAACAGCATTGAGGACATCTTGCTGCAGTACCCTGATTGGAGAGGGCACCCGTTCCTGC
AAGAAGAAGTGGCCCAGTTCCTGGCCTACTAGTGCAAGGCACCTGCCCGACTTGATCCAGAAAATGTGGTTGTTCTAAAT
GGCTGCTGCTCTGTCTTCTCTGCACTGGCCATGGTTCTGTGTGATCCAAGCGAGGCCTTCCTGGCGCCTGCTCCCTTCTA
TAGTGGCTTTGACTTTAGCTCCTGCCTGTACGTGAAGGTTGAGTTGATTCCTGTCCACCTGGAGAGTGAGATCACTGTTG
CAAACACCCATCCATTCCACCTTGCTATGGACAAGTTAGAGGAAGCCCTGCTTAAAGCTAGGGTTGAGAGGAAAAAGGTC
CGAGGCCTTGTGCTAATCAACCCTCAGAGTCTTCTGGGTGACATCTGCTCCTCAGACTCGCGATGGAATACCTGGAATTT
GCCAAGAGGTATAACCTACATGTGATCATAGATGAGATTTACATGCTCTCTGTGTTT

Alignment

ORF - retro_ptro_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.57 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHRSDTLPVPSGQRRGRVPRDHSIYTQLL-EITLHLQQAMTEHFVQLTSRQG-LSLEERRHTEAICEHE
          MSH.SDTLPVPSGQ.RG.V.RD.SIYTQLL.E..LHLQ..M.E.FVQL.SRQG.L.LEE.RHT.A..EHE
Retrocopy MSHQSDTLPVPSGQMRGQVLRDQSIYTQLL<EMMLHLQ*TMREYFVQLMSRQG>LPLEEWRHTQAVREHE

Parental  ALLSRLICRMINLLQSGATSGLELQVPLPSEDSRGDVRYGQRAQLSGQPDPVPQLSDCEAAFVSHDLSNR
          ALL.RL.C.MI.LL.SGA.SGLELQVPLPS.DSRGDVRYGQ.AQLS.QPDPVPQLSDCEAAF.S.DLSN.
Retrocopy ALLGRLMCQMIQLL*SGAISGLELQVPLPSQDSRGDVRYGQGAQLSRQPDPVPQLSDCEAAFISRDLSNC

Parental  GIDISVFYQSSFQDYNAYQKDKYHKDKNTLGFINLGTSENKLCMDLMTERLQESDMNCTEDTLLQYPDWR
          GIDISVFY.SSFQDYNAYQKDKYHKDKNTL.F.NLGTSENKLC.DLMTERLQESD.N..ED.LLQYPDWR
Retrocopy GIDISVFY*SSFQDYNAYQKDKYHKDKNTLSFVNLGTSENKLCIDLMTERLQESDTNSIEDILLQYPDWR

Parental  GQPFLREEVARFLTYYCRAPTRLDPENVVVLNGCCSVFSALAMVLCDPGEAFLVPAPFYGGFAFSSRLYA
          G.PFL.EEVA.FL.Y.C.AP.RLDPENVVVLNGCCSVFSALAMVLCDP.EAFL.PAPFY.GF.FSS.LY.
Retrocopy GHPFLQEEVAQFLAY*CKAPARLDPENVVVLNGCCSVFSALAMVLCDPSEAFLAPAPFYSGFDFSSCLYV

Parental  KVELIPVHLESEVTVTNTHPFQLTVDKLEEALLEARLEGKKVRGLVLINPQNPLGDIYSPES-LMKYLEF
          KVELIPVHLESE.TV.NTHPF.L..DKLEEALL.AR.E.KKVRGLVLINPQ..LGDI.S..S..M.YLEF
Retrocopy KVELIPVHLESEITVANTHPFHLAMDKLEEALLKARVERKKVRGLVLINPQSLLGDICSSDS<AMEYLEF

Parental  AKRYNLHVIIDEIYMLSVF
          AKRYNLHVIIDEIYMLSVF
Retrocopy AKRYNLHVIIDEIYMLSVF

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	0.00 RPM	0.14 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.03 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.21 RPM	0.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2414 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2414 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3553
Pongo abelii	retro_pabe_2934

---

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,