RetrogeneDB ID: retro_ptro_1576

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:18761390..18762005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSPTRG00000011484
• Aliases: None
• Description: None

Sequence

>retro_ptro_1576
TTAAAGGAAGAGCCTAGGCTGGATGTCTTGATCAATAACGCAGGGATCTTCCAGTGCCCTTACATGAAGACTGAAGATGG
GTTTGAGATGCAGTTCGGAGTGAACCATCTGGGGCACTTTCTACTCACCAATCTTCTCCTTGGACTCCTCAAAAGTTCAG
CTCCCAGCAGGATTGTGGTAGTTTCTTCCAAACTTTATAAATACGGAGACATCAACTTTGATGACTTGAACAGTGAACAA
AGCTATAATAAAAGCTTTTGTTATAGCCGGAGCAAACTGGCTAACATTCTTTTTACCAGGGAACTAGCCCGCCGCTTAGA
AGGCACAAATGTCACCGTCAATGTGTTGCATCCTGGTATTGTACGGACAAATCTGGGGAGGCACATACACATTCCACTGT
TGGTCAAACCACTCTTCAATTTGGTGTCATGGGCTTTTTTCAAAACTCCAGTAGAAGGTGCCCAGACTTCCATTTATTTG
GCCTCTTCACCTGAGGTAGAAGGAGTGTCAGGAAGATACTTTGGGGATTGTAAAGAGGAAGAACTGTTGCCCAAAGCTAT
GGATGAATCTGTTGCAAGAAAACTCTGGGATATCAGTGAAGTGATGGTTGGCCTG

Alignment

ORF - retro_ptro_1576 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.33 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEEEERVDILINNAGVMRCPHWTTEDGFEMQFGVNHLGHFLLTNLLLDKLKASAPSRIINLSSLAHVAGH
          ..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  TLGPIFWLLVKSPELAAQPSTYLAVAEELADVSGKYFDGLKQKAPAPEAEDEEVAQRLWAESARLVGL
          ......W...K.P...AQ.S.YLA...E...VSG.YF...K.....P.A.DE.VA..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	5.27 RPM	8.60 RPM
SRP007412_cerebellum	4.77 RPM	10.43 RPM
SRP007412_heart	10.20 RPM	8.63 RPM
SRP007412_kidney	8.87 RPM	17.78 RPM
SRP007412_liver	6.15 RPM	7.17 RPM
SRP007412_testis	14.96 RPM	5.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1576 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1576 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1972
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,