RetrogeneDB ID: retro_pabe_126

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:50320295..50320823(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005795
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSPPYG00000004473
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5R5P7]

Sequence

>retro_pabe_126
ATGGGGAAGGTGCTATCCAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGCCTGGACGCGGCCGGCAAGAC
AACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATTCCCACTGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAATGTCAAGTTCAACGTATGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACTGGG
ACCCAAGGTCTCATCTTCGTAGTGGACTGCGCCGACCGCGACCGCATCGATGAGGCTCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCTTAA

Alignment

ORF - retro_pabe_126 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
Retrocopy GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
          PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
Retrocopy PLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL

Parental  HSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
          ...R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy TRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	5.97 RPM	736.91 RPM
SRP007412_cerebellum	5.59 RPM	177.42 RPM
SRP007412_heart	4.18 RPM	23.93 RPM
SRP007412_kidney	14.12 RPM	203.72 RPM
SRP007412_liver	15.82 RPM	54.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_126 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_126 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
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 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28, retro_amel_70,
Canis familiaris	ENSCAFG00000008767	1 retrocopy	retro_cfam_119,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Myotis lucifugus	ENSMLUG00000029846	1 retrocopy	retro_mluc_119,
Macaca mulatta	ENSMMUG00000006968	1 retrocopy	retro_mmul_174,
Mustela putorius furo	ENSMPUG00000014730	1 retrocopy	retro_mputfur_86,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126 ,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Pteropus vampyrus	ENSPVAG00000004626	1 retrocopy	retro_pvam_7,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,