RetrogeneDB ID: retro_pabe_1972

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:93796866..93797481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSPPYG00000010398
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_pabe_1972
TTAAAGGAAGAGCCTAGGCTGGATGTCTTGATCAATAACGCAGGGATCTTCCAGTGCCCTTACATGAAGACTGAAGATGG
GTTTGAGATGCAGTTTGGAGTGAACCATCTGGGGCACTTTCTACTCACCAATCTGCTCCTTGGACTCCTCAAAAGTTCAG
CTCCCAGCAGGATTGTGGTAGTTTCTTCCAAACTTTATAAATACGGAGACATCAACTTTGATGACTTGAACAGTGAACAA
AGCTATAATAAAAGCTTTTGTTATAGCCGGAGCAAACTGGCTAACATTCTTTTTACCAGGGAACTAGCCCGCCGCTTAGA
AGGCACAAATGTTACCGTCAATGTGTTGCATCCTGGTATTGTACGGACAAATCTGGGGAGGCACATACACATTCCACTGT
TGGTCAAACCACTCTTCAATTTGGTGTCATGGGCTTTTTTCAAAACTCCAGTAGAAGGTGCCCAGACTTCCATTTATTTG
GCCTCTTCACCTGAGGTAGAAGGAGTGTCAGGAAGATACTTTGGGGATTGTAAAGAGGAAGAACTATTGCCCAAAGCTAT
GGATGAATCTGTTGCAAGAAAACTCTGGGATATCAGTGAAGTGATGGTTGGCCTG

Alignment

ORF - retro_pabe_1972 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.81 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEEEERVDILINNAGVMRCPHWITEDGFEMQFGVNHLGHFLLTNLLLNKLKASAPSRIINLSSLAHVAGH
          ..EE.R.D.LINNAG...CP...TEDGFEMQFGVNHLGHFLLTNLLL..LK.SAPSRI...SS.....G.
Retrocopy LKEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGD

Parental  IDFDDLNWQTRKYNTKAAYCQSKLAIVLFTKELSRRLQGSGVTVNALHPGVARTELGRHTGIHGSTFSST
          I.FDDLN.....YN....Y..SKLA..LFT.EL.RRL.G..VTVN.LHPG..RT.LGRH..IH.......
Retrocopy INFDDLN-SEQSYNKSFCYSRSKLANILFTRELARRLEGTNVTVNVLHPGIVRTNLGRH--IHIPLLVKP

Parental  TLGPIFWLLVKSPELAAQPSTYLAVAEELADVSGKYFDGLKQKAPAPEAEDEEVARRLWAESARLVGL
          ......W...K.P...AQ.S.YLA...E...VSG.YF...K.....P.A.DE.VAR.LW..S...VGL
Retrocopy LFNLVSWAFFKTPVEGAQTSIYLASSPEVEGVSGRYFGDCKEEELLPKAMDESVARKLWDISEVMVGL

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	5.86 RPM	3.21 RPM
SRP007412_cerebellum	7.90 RPM	2.92 RPM
SRP007412_heart	11.29 RPM	1.87 RPM
SRP007412_kidney	5.14 RPM	3.51 RPM
SRP007412_liver	4.99 RPM	2.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1972 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1972 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1576
Equus caballus	retro_ecab_338

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972 ,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,