RetrogeneDB ID: retro_pabe_3090

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:125916342..125917144(+)
• Located in intron of: ENSPPYG00000017990

Retrocopy information

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

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSPPYG00000012654
• Aliases: None
• Description: ornithine decarboxylase 1 [Source:HGNC Symbol;Acc:8109]

Sequence

>retro_pabe_3090
TTCCTTGATGAAGGTTTTACTAACAAGGACATTCTGGACCAAAAAATTAATGAATTTTCTTCTGATGATGATTAGGATGC
CTTCTATGTCATGGACCTTAGAGACATTCTAAAGGCACATCTAAGATGGTTAAAAGCTCTTCTTCATGTCACCCCCTTTT
ATGCAGTCAAATATAATGACAGCAGAGCCATCATCAAGACTCTTGCTGCCATCGGGACAGGATTTGACTGTGCTAGCAAG
GCTGAAATACAATTGGTGCAGATTCTGGGGATGCCCCCAGAGAGGTTTATCTATGCAAATTCTTGTAAACAAATGTCTCA
AATTAAGTACACTGCCAATAATGGAGTCCAGATGATGATTTTCGGTAATGAGGTCAAGTTGATGTCAGTTGCCAGAACAC
ACTCAAAGCAGAGTTGGTTTTTAAGATTGCAAATGATGATTCCAAAGCAGCCCGTCACGTCAGTGTTAAATCTGGTGCCA
TGCTCAAAGCCAGCAGGCTTCTTCTGGAATGGGCAAAAGAGCTAAATATTGATGTCACTGGTGTCAGCTTCCATGTAGGA
AGTAGCTGTACCAATCCTGAGACCTTCATGCAGGCAGCCTCCAATGTCCACTATGTCTTTGACACAGGAGTTGAGTTTGG
TTTCAGAATGTAACTGCTTAATACTGGCAGTTGCTTTCCTGGATCTGAGGATGTGAGGCTTAAATCTGAAGTATTACCAG
TGTAATCAACCCAGCATCGGACAAGTATTTTCCACCAGACTCTAGAGAGAGAGTCACAGCTGAGCCAGGCAGATATTTCA
TG

Alignment

ORF - retro_pabe_3090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKAVPRVTPFYAVKCNDSKAIVKTLAA
          FLDEGFT.KDILDQKINE.SS.DD.DAFYV.DL.DILK.HLRWLKA...VTPFYAVK.NDS.AI.KTLAA
Retrocopy FLDEGFTNKDILDQKINEFSSDDD*DAFYVMDLRDILKAHLRWLKALLHVTPFYAVKYNDSRAIIKTLAA

Parental  VGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHP-KAKL
          .GTGFDCASK.EIQLVQ.LG.PPER.IYAN.CKQ.SQIKY.ANNGVQMM.F..EV.LM.VAR.H..KA.L
Retrocopy IGTGFDCASKAEIQLVQILGMPPERFIYANSCKQMSQIKYTANNGVQMMIFGNEVKLMSVARTHS<KAEL

Parental  VLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDM
          V..IA.DDSKA....SVK.GA.L..SRLLLE.AKELNIDV.GVSFHVGS.CT.PETF.QA.S....VFD.
Retrocopy VFKIANDDSKAARHVSVKSGAMLKASRLLLEWAKELNIDVTGVSFHVGSSCTNPETFMQAASNVHYVFDT

Parental  GAEVGFSMYLLDIGGGFPGSEDVKLKFE-EITSVINPALDKYFPSDSGVRIIAEPGRYYV
          G.E.GF.M.LL..G..FPGSEDV.LK.E..ITSVINPA.DKYFP.DS..R..AEPGRY..
Retrocopy GVEFGFRM*LLNTGSCFPGSEDVRLKSE<SITSVINPASDKYFPPDSRERVTAEPGRYFM

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	29.75 RPM
SRP007412_cerebellum	0.49 RPM	21.65 RPM
SRP007412_heart	0.09 RPM	37.75 RPM
SRP007412_kidney	0.23 RPM	188.87 RPM
SRP007412_liver	0.15 RPM	149.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3090 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3090 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1645
Callithrix jacchus	retro_cjac_3170

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090 ,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,