RetrogeneDB ID: retro_ptro_5

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:48809128..48809656(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000006324
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSPTRG00000002066
• Aliases: None
• Description: None

Sequence

>retro_ptro_5
ATGGGGAAGGTGCTATCCAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGCCTGGACGCGGCCGGCAAGAC
AACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATTCCCACTGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAATGTCAAGTTCAACGTATGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACTGGG
ACCCAAGGTCTCATCTTCGTAGTGGACTGCGCCGACCGCGACCGCATCGATGAGGCTCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCTTAA

Alignment

ORF - retro_ptro_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 92.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHY
          .FG.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIRPLWRHY
Retrocopy IFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHY

Parental  FQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHR
          ...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL...R.R
Retrocopy YTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDR

Parental  NWYIQATCATSGDGLYEGLDWLSNQLRN
          NWY.Q..CATSGDGLYEGL.WL......
Retrocopy NWYVQPSCATSGDGLYEGLTWLTSNYKS

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	8.70 RPM	207.11 RPM
SRP007412_cerebellum	9.39 RPM	87.58 RPM
SRP007412_heart	4.55 RPM	56.54 RPM
SRP007412_kidney	23.85 RPM	135.31 RPM
SRP007412_liver	15.75 RPM	111.23 RPM
SRP007412_testis	6.22 RPM	77.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_5 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_5 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_5 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Mus musculus	retro_mmus_147
Rattus norvegicus	retro_rnor_272
Oryctolagus cuniculus	retro_ocun_132
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119
Equus caballus	retro_ecab_106

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dipodomys ordii	ENSDORG00000007603	4 retrocopies	retro_dord_31, retro_dord_351, retro_dord_409, retro_dord_573,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5 ,
Pan troglodytes	ENSPTRG00000015051	2 retrocopies	retro_ptro_2866, retro_ptro_888,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,