RetrogeneDB ID: retro_pabe_3389

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:25615912..25616391(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSPPYG00000002530
• Aliases: None
• Description: phosphoglycerate mutase 1 [Source:RefSeq peptide;Acc:NP_001127164]

Sequence

>retro_pabe_3389
ATGGTCACCTACAAGCTAGTACTGATCAGGTGTGGTGAGAGCATGTGGAACCTGGAGAATCACTTCAGCAGCTGGTACAA
TGCCAATCTAATCCCGGTAGGCCACAAGGAGGCAAAGCGCAGCAGGCAGGCTCTGCGAGATGCTGGCTATGAGTTTGACA
TCTGCTTCCCCTCAGTGCAGAAGTGAGCGATCGGACCCTCTGGACAGTGCAAAATGCCATTGATCAGATGCGGCTGCCAG
TAGTGAGGACTTGGTGCCTCAAGGAGTGGCATTATGGGGGTCTGACTGGCCTCAATAAAGCAGAAACTTCTGTGAAGCAT
GGTGAGACCCAGGTGAAGATCTGGAGGCGCTCCTGTGATGTCCCACCACCTCCGATGGAACCCGACCATCCTTTGTACAG
CAACATCAGTAAGGATTGCAGGTATGCAGACCTCACTGAAGATCAGCTATCCTCCGGTGAGAGTCTGAAGGAAATAGTT

Alignment

ORF - retro_pabe_3389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 62.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAI-RTLWT
          M..YKLVLIR.GES.WNLEN.FS.WY.A.L.P.GH.EAKR..QALRDAGYEFDICF.SVQK.AI.RTLWT
Retrocopy MVTYKLVLIRCGESMWNLENHFSSWYNANLIPVGHKEAKRSRQALRDAGYEFDICFPSVQK*AI<RTLWT

Parental  VLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKD
          V..AIDQM.LPVVRTW.L.E.HYGGLTGLNKAET..KHGE.QVKIWRRS.DVPPPPMEPDHP.YSNISKD
Retrocopy VQNAIDQMRLPVVRTWCLKEWHYGGLTGLNKAETSVKHGETQVKIWRRSCDVPPPPMEPDHPLYSNISKD

Parental  RRYADLTEDQLPSCESLKDTI
          .RYADLTEDQL.S.ESLK...
Retrocopy CRYADLTEDQLSSGESLKEIV

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	0.06 RPM	414.74 RPM
SRP007412_cerebellum	0.00 RPM	300.72 RPM
SRP007412_heart	0.00 RPM	42.14 RPM
SRP007412_kidney	0.00 RPM	141.90 RPM
SRP007412_liver	0.00 RPM	89.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3389 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3389 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4249
Gorilla gorilla	retro_ggor_2849

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Myotis lucifugus	ENSMLUG00000009117	6 retrocopies	retro_mluc_1280, retro_mluc_1595, retro_mluc_1741, retro_mluc_2246, retro_mluc_632, retro_mluc_745,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furo	ENSMPUG00000017045	1 retrocopy	retro_mputfur_1409,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389 , retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,