RetrogeneDB ID: retro_pabe_1535

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:13898438..13898956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRTO4
• Ensembl ID: ENSPPYG00000001795
• Aliases: None
• Description: mRNA turnover 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:18477]

Sequence

>retro_pabe_1535
ATGCCCAAATCCAAGCGCGACAAGAAAGTCTCCTTAACTAAAACTGCCAAGAAAGGCTTGGAATTGAAACAAAACCTGAT
AGAAGAGCTTTGGAAATGTGTGGACACCTACAGTACCTTTTCATCTTCTCTGTGGCCAACATGAGGAACAGCAGGCTGAA
GGACATCCAGAACACCTGAAAGCACAGCTGGATGTTCTTTGGCAAAAACAAGGTGATGATGGTGGCCTTGGGTCAGAGCC
CACCTGATGAGAACAAAGATAACCTGCACCACGTCAGCAAAAGGTTGAGGCGTGAAGTGGGTCTCCTGTTCACCAACCGC
ACAAAGGAGGAAGTGAATGAATGGTTTACGAAATGCACAGAAATGGACTACACCCGAGCTGGTAACAAAGCAGCTTTCAC
TGCAAGCCTGGACTCAGGGCCCCTGGAGCAGTTCCCCAACTCCATGGAGCCACAGCTCACGCAGCTGGCCCTGCCCACTG
CCCTCGAGAGAGGTGTGCTGTCCAATTATGAGGTGTGC

Alignment

ORF - retro_pabe_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.88 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTY-KYLFIFSVANMRNSKLKDIRNAWKHSRMFFGK
          MPKSKRDKKVSLTKTAKKGLELKQNLIEEL.KCVDTY..YLFIFSVANMRNS.LKDI.N..KHS.MFFGK
Retrocopy MPKSKRDKKVSLTKTAKKGLELKQNLIEELWKCVDTY<QYLFIFSVANMRNSRLKDIQNT*KHSWMFFGK

Parental  NKVMMVALGRSPSDEYKDNLHQVSKRLRGEVGLLFTNRTKEEVNEWFTKYTEMDYARAGNKAAFTVSLDP
          NKVMMVALG.SP.DE.KDNLH.VSKRLR.EVGLLFTNRTKEEVNEWFTK.TEMDY.RAGNKAAFT.SLD.
Retrocopy NKVMMVALGQSPPDENKDNLHHVSKRLRREVGLLFTNRTKEEVNEWFTKCTEMDYTRAGNKAAFTASLDS

Parental  GPLEQFPHSMEPQLRQLGLPTALKRGVVTLLSDYEVC
          GPLEQFP.SMEPQL.QL.LPTAL.RGV...LS.YEVC
Retrocopy GPLEQFPNSMEPQLTQLALPTALERGV---LSNYEVC

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	0.00 RPM	11.33 RPM
SRP007412_cerebellum	0.00 RPM	7.54 RPM
SRP007412_heart	0.00 RPM	4.12 RPM
SRP007412_kidney	0.00 RPM	9.78 RPM
SRP007412_liver	0.00 RPM	15.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1535 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1535 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1766
Pan troglodytes	retro_ptro_1182
Gorilla gorilla	retro_ggor_2244

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015189	1 retrocopy	retro_cfam_1353,
Callithrix jacchus	ENSCJAG00000006812	3 retrocopies	retro_cjac_1146, retro_cjac_1834, retro_cjac_3791,
Dasypus novemcinctus	ENSDNOG00000010119	6 retrocopies	retro_dnov_1051, retro_dnov_1545, retro_dnov_170, retro_dnov_1890, retro_dnov_2044, retro_dnov_2255,
Echinops telfairi	ENSETEG00000001675	5 retrocopies	retro_etel_1080, retro_etel_1162, retro_etel_1172, retro_etel_1887, retro_etel_2177,
Homo sapiens	ENSG00000053372	2 retrocopies	retro_hsap_1766, retro_hsap_1914,
Gorilla gorilla	ENSGGOG00000000533	2 retrocopies	retro_ggor_1400, retro_ggor_2244,
Macropus eugenii	ENSMEUG00000000027	1 retrocopy	retro_meug_1606,
Microcebus murinus	ENSMICG00000004019	2 retrocopies	retro_mmur_1235, retro_mmur_733,
Myotis lucifugus	ENSMLUG00000001566	1 retrocopy	retro_mluc_374,
Macaca mulatta	ENSMMUG00000006695	1 retrocopy	retro_mmul_107,
Monodelphis domestica	ENSMODG00000015874	1 retrocopy	retro_mdom_1694,
Mustela putorius furo	ENSMPUG00000016181	2 retrocopies	retro_mputfur_1177, retro_mputfur_1430,
Mus musculus	ENSMUSG00000028741	2 retrocopies	retro_mmus_852, retro_mmus_924,
Oryctolagus cuniculus	ENSOCUG00000000274	2 retrocopies	retro_ocun_1191, retro_ocun_951,
Otolemur garnettii	ENSOGAG00000010713	2 retrocopies	retro_ogar_1826, retro_ogar_2060,
Pongo abelii	ENSPPYG00000001795	2 retrocopies	retro_pabe_1535 , retro_pabe_1548,
Pan troglodytes	ENSPTRG00000000262	2 retrocopies	retro_ptro_1182, retro_ptro_1248,
Rattus norvegicus	ENSRNOG00000017979	1 retrocopy	retro_rnor_2967,
Ictidomys tridecemlineatus	ENSSTOG00000028112	1 retrocopy	retro_itri_1551,
Tupaia belangeri	ENSTBEG00000006502	8 retrocopies	retro_tbel_1020, retro_tbel_1189, retro_tbel_1210, retro_tbel_1873, retro_tbel_1945, retro_tbel_2665, retro_tbel_394, retro_tbel_559,