RetrogeneDB ID: retro_pabe_2838

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:16534572..16535048(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSPPYG00000004947
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_pabe_2838
ATGCTGGCTTACCAATCTTCTCTCATGGACCCTGACACCAAACTCACTGGAAACATGGCACTGTTACCCATCAGAAGCCA
ATTTAAAGGACCTGACCCCAGAGAGACAAAAGATACAGATATTGTGGATGAAGCCATCTATTACTTCAAGGCCAATGTCT
TCTTCAAAAACTATGAAATTAAGAATGAAGCTGATAGGACCTTGATATATATATAACTCTCTACATTTCTGAGTGTTCGA
AGGGACTCCAAAAGTACAAATCCAAAATCCAAGGTGAGAAAGAAATGTATACATTGGGAATCACGAATTTTCCTATCCCT
GGAGAGCCTCATTTTCCACTTAACGCAATTTATGCCAAACCTGCAAACAAACAGGAAGATGAAGTGATGAGAGCCTATTT
ACAACAGCTAAGGAGAAAGACTGGACTGAGACCTTGTGAGAAAGTTTTTGACCCTCAGAATGATAAACCCAGCAAG

Alignment

ORF - retro_pabe_2838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 94.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
          M.AY.SSLMDPDTKL.GNMALLPIRSQFKGP.PRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
Retrocopy MLAYQSSLMDPDTKLTGNMALLPIRSQFKGPDPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY

Parental  ITLYISECLKKLQK-CNSKS-QGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQ
          I.L..........K..N.KS.QGEKEMYTLGITNFPIPGEP.FPLNAIYAKPANKQEDEVMRAYLQQLR.
Retrocopy I*LSTFLSVRRDSKSTNPKS<QGEKEMYTLGITNFPIPGEPHFPLNAIYAKPANKQEDEVMRAYLQQLRR

Parental  ETGLRLCEKVFDPQNDKPSK
          .TGLR.CEKVFDPQNDKPSK
Retrocopy KTGLRPCEKVFDPQNDKPSK

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	0.44 RPM	14.76 RPM
SRP007412_cerebellum	0.00 RPM	12.40 RPM
SRP007412_heart	0.24 RPM	6.35 RPM
SRP007412_kidney	0.66 RPM	16.81 RPM
SRP007412_liver	0.67 RPM	17.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2838 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2838 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3425

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Dasypus novemcinctus	ENSDNOG00000004987	2 retrocopies	retro_dnov_2619, retro_dnov_685,
Dipodomys ordii	ENSDORG00000008212	1 retrocopy	retro_dord_312,
Erinaceus europaeus	ENSEEUG00000011531	2 retrocopies	retro_eeur_122, retro_eeur_99,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Loxodonta africana	ENSLAFG00000006166	3 retrocopies	retro_lafr_1119, retro_lafr_763, retro_lafr_840,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Nomascus leucogenys	ENSNLEG00000002802	4 retrocopies	retro_nleu_239, retro_nleu_283, retro_nleu_3078, retro_nleu_389,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Otolemur garnettii	ENSOGAG00000013424	1 retrocopy	retro_ogar_2855,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Procavia capensis	ENSPCAG00000011858	2 retrocopies	retro_pcap_421, retro_pcap_441,
Pongo abelii	ENSPPYG00000004947	6 retrocopies	retro_pabe_1735, retro_pabe_1790, retro_pabe_2838 , retro_pabe_376, retro_pabe_769, retro_pabe_792,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Tupaia belangeri	ENSTBEG00000011219	1 retrocopy	retro_tbel_2268,
Tarsius syrichta	ENSTSYG00000002953	4 retrocopies	retro_tsyr_1150, retro_tsyr_1341, retro_tsyr_2103, retro_tsyr_794,
Tursiops truncatus	ENSTTRG00000015083	2 retrocopies	retro_ttru_713, retro_ttru_880,
Vicugna pacos	ENSVPAG00000008404	1 retrocopy	retro_vpac_225,