RetrogeneDB ID: retro_pabe_2864

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:47617553..47618036(+)
• Located in intron of: ENSPPYG00000016677

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSPPYG00000006360
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 17 [Source:HGNC Symbol;Acc:25556]

Sequence

>retro_pabe_2864
GAGGCCCAGGCCCAGGTGAGTGAGAAGGTGGAGGAAAGCTAGAGCACCAGGACACTTGAGCAGGAGATTGAACATCTTAG
TGAATAGTGTTCCTGGCAGCTGGAGGAACAGCAGATGATGATCCAGGAGCAGATGTGCCAGGAACTTGACTTGAGATTGA
AGGTCAGAAAATACTGAAGACAAAGGAACCCAAAACTAAAACTGAAATGGAAGTGCAGGAAGGATGAGTCAGAAGGCAGG
TACTCCAAAGGTGTCCTCTTGGGGCTTTTGCGAAAGTATGGTGGAATTCTCAACCTGGTGCTTTTGAGTAAGAAGGCAGG
TACTGGTGTCATGAAGTTTGGGACTGTTGAGGCTGCAGAGATGGCTGTCTGGAATAAAGTTGGCCTGGGTGATAATCCTC
GAAAAATTTCCTCTTTCAAAGGAAGACTCCGGGGTGCAGTGGGCCCCAGCCACCCAGGACAGTGAAGGGACCCAGTGGTG
TCT

Alignment

ORF - retro_pabe_2864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.76 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAQAQESDDEEESRSTRTLEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAESTEGQGTPKLKL
          .AQAQ.S...EES.STRTLEQEIE.L.E..S.QLEEQQ..I.EQ..QE.D.RL..K......Q..PKLKL
Retrocopy EAQAQVSEKVEES*STRTLEQEIEHLSE*CSWQLEEQQMMIQEQMCQELDLRL--KVRKY*RQRNPKLKL

Parental  KWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEAGLVDNPLKIS
          KWKC.K.DES.G.YSK.VLL.LL.KYG..LNLVL.SKK.GT.V..F.TV.AAE.AV.N..GL.DNP.KIS
Retrocopy KWKCRK-DESEGRYSKGVLLGLLRKYGGILNLVLLSKKAGTGVMKFGTVEAAEMAVWNKVGLGDNPRKIS

Parental  WLEGQPQDAMGRSHSGLSKGSVLS
          ...G....A.G.SH.G.....V.S
Retrocopy SFKGRLRGAVGPSHPGQ*RDPVVS

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	7.91 RPM
SRP007412_cerebellum	0.00 RPM	20.31 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.03 RPM	18.20 RPM
SRP007412_liver	0.00 RPM	19.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2864 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2864 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3468
Pan troglodytes	retro_ptro_2351
Gorilla gorilla	retro_ggor_2340

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864 ,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,