RetrogeneDB ID: retro_ptro_2782

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:99812604..99813095(-)
• Located in intron of: ENSPTRG00000020479

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC14
• Ensembl ID: ENSPTRG00000029747
• Aliases: SARNP, DNAJC14
• Description: None

Sequence

>retro_ptro_2782
GAAGAGGCAAATGAAGATGTACTGGGAGATGAAACAGAGGAAGAAGAAACAAAGCCCCATAGAAATCCCTGTCAAAGAGG
AAGAACTCCCTGAAAAAACTGTTGACGTGGAAGCAGAGAAGAAAGTGGTAAAAATTACATCTGAAATACCACAGGGAGAG
AGAATGCAGAAGAGGGCTGAACAAGTCCATGTACCTGTGAGCTTGTAAAGTAAGAAAACTGCCCGGGCAGCTAGGTTTGG
GACTTCTTCAGTTTCAACAAAAGGTCTGTCATCTAACAACAAACCTATCAAGAAACCTGGATAAGCTAAAGGAAAGAGCT
CAAAGATTTGGTTTGAATGGCTCTTCAATCTCCAGAAAGTCTGAAGATGATGAGAAACTGAAAAGGAGGCAGGACTGATT
TGGGATTATCACTGGTTCAGCTGGAACCAGAAGGAACACAGAGGATACAGAGGCAAAGAATAGGAAAAGAGCCGCGCGCT
ATGGGATTGCC

Alignment

ORF - retro_ptro_2782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 77.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEANEEDVLGDETEEEETKP-IELPVKEEEPPEKTVDVAAEKKVVKITSEIPQTERMQKRAERFNVPVSL
          EEANE.DVLGDETEEEETKP.IE.PVKEEE.PEKTVDV.AEKKVVKITSEIPQ.ERMQKRAE...VPVSL
Retrocopy EEANE-DVLGDETEEEETKP>IEIPVKEEELPEKTVDVEAEKKVVKITSEIPQGERMQKRAEQVHVPVSL

Parental  ESKKAARAARFGISSVPTKGLSSDNKPMV-NLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVT
          .SKK.ARAARFG.SSV.TKGLSS.NKP...NLDKLKERAQRFGLN.SSISRKSEDDEKLK.R...FGI.T
Retrocopy *SKKTARAARFGTSSVSTKGLSSNNKPIK>NLDKLKERAQRFGLNGSSISRKSEDDEKLKRRQD*FGIIT

Parental  SSAGT-GTTEDTEAKKRKRAERFGIA
          .SAGT...TEDTEAK.RKRA.R.GIA
Retrocopy GSAGTRRNTEDTEAKNRKRAARYGIA

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	17.05 RPM
SRP007412_cerebellum	0.00 RPM	21.40 RPM
SRP007412_heart	0.00 RPM	26.76 RPM
SRP007412_kidney	0.00 RPM	26.73 RPM
SRP007412_liver	0.00 RPM	18.95 RPM
SRP007412_testis	0.00 RPM	73.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2782 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2782 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3358
Callithrix jacchus	retro_cjac_1487

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Callithrix jacchus	ENSCJAG00000007853	8 retrocopies	retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560, retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Dipodomys ordii	ENSDORG00000001065	1 retrocopy	retro_dord_80,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Homo sapiens	ENSG00000205323	1 retrocopy	retro_hsap_3882,
Gorilla gorilla	ENSGGOG00000013217	2 retrocopies	retro_ggor_2613, retro_ggor_2753,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Microcebus murinus	ENSMICG00000010902	1 retrocopy	retro_mmur_358,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Nomascus leucogenys	ENSNLEG00000017599	2 retrocopies	retro_nleu_2779, retro_nleu_569,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45,
Pongo abelii	ENSPPYG00000004630	2 retrocopies	retro_pabe_3116, retro_pabe_3358,
Pan troglodytes	ENSPTRG00000029747	2 retrocopies	retro_ptro_2644, retro_ptro_2782 ,
Rattus norvegicus	ENSRNOG00000030520	2 retrocopies	retro_rnor_1326, retro_rnor_471,