RetrogeneDB ID: retro_ptro_2640

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:78240744..78241065(-)
• Located in intron of: ENSPTRG00000019338

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3C
• Ensembl ID: ENSPTRG00000009655
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:G2HIR8]

Sequence

>retro_ptro_2640
CCGCAAATCGACCAGTGTAGTAAAGCAGCCAGAAGGCCGCTCACAAAAGTGTGCCCTCTACTGGAAGGGTGAAGACACAT
CATAACAGGCCTGGTATTCCATGAAACTACAGGTTATCAGAAGTCCACTGAATCACTGACTCGCAAACTTCCCTTCCAGT
GTCTGGTGCAACAAATTGCTCAGGGCTTTAAAACACATCTATGCTTCTAGAGTGCAGTTATTGGTGCTTTGCAGGAGGCA
AGTGAGGCTTAACTGGTTGGCCATTTTTGAGACACCAACCTGTGTGCTATCCATGCAAAACGTGTAACAATTATGCCAAA
A

Alignment

ORF - retro_ptro_2640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 78.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQ
          P......KAAR.............R.........E...YQKSTE.L.RKLPFQ.LV..IAQ.FKT.L.F.
Retrocopy PQIDQCSKAARRPLTKVCPLLEG*RHIITGLVFHETTGYQKSTESLTRKLPFQCLVQQIAQGFKTHLCF*

Parental  SAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK
          SA.IGALQEASEA.LVG.F.DTNLCAIHAKRVTIMPK
Retrocopy SAVIGALQEASEA*LVGHF*DTNLCAIHAKRVTIMPK

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	0.04 RPM	121.81 RPM
SRP007412_cerebellum	0.04 RPM	340.56 RPM
SRP007412_heart	0.00 RPM	83.18 RPM
SRP007412_kidney	0.00 RPM	177.83 RPM
SRP007412_liver	0.07 RPM	141.18 RPM
SRP007412_testis	0.00 RPM	690.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2640 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000002045	20 retrocopies	retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098, retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640 , retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,