RetrogeneDB ID: retro_pabe_3058

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:44504894..44505720(+)
• Located in intron of: ENSPPYG00000025822

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSPPYG00000005810
• Aliases: TMX1, TXNDC1
• Description: thioredoxin-related transmembrane protein 1 precursor [Source:RefSeq peptide;Acc:NP_001126776]

Sequence

>retro_pabe_3058
ATAGCGCCCTCCAGGAGTCTTGCAGTTCCCCTGGCAGTCCTGGTACTGTTGCTTTGGGGTGCTCCCTGGACCCACTGGCG
GCAGAGCAATGTACACATCATCACGGACGAGAACTGGAGAGAGCTGCTGGAAGGAGGCTGGATGATAGAATTTTATGCCC
CGTGGTGCCCTGCTTGTCAAAGCCATCAACCGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTGAGGTTAATGTTG
TGAAAGTAGATGTCACAGAGCAGCCAGGACTGACTGGACAGTTTACAATAACTGCTCTTCCTACTATTTATCATTGTAAA
GATGGTGAATTTAGGCATCCTCAGGGTCCAAGGACTAAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAG
TATTGAACCCGTTTCATCATGGTTTGGTCCAGGTTCTGTTCAGATGAGTAGTACGTCAGCACTCTTTCAGCTATCTATGT
GGATCAGGACTTGCCATAACTACTTTATTGAAGACCTTGGATTGCCAGTGTGGGGATCATATGCTGTTTTTCCTTTAGCA
ACTCTGCATTGTGGACTGTTACTAGGACTCTGTATGATATTTGTGGCAGATTGCCTTTGTCCTTCAGAAAGGCACAGACC
ACAGCCATACCCTTCAAAAAAATTATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGCTGATA
AAGAAGATGTTTCAGAAGAAGAAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAAGACAACACTCTC
TGGGTCCATCACTGGCCACAGATAAA

Alignment

ORF - retro_pabe_3058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.9 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPSGSLAVPLAVLVLLLWGAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFA
          .APS.SLAVPLAVLVLLLWGAPWTH.R.SNV..ITDENWRELLEG.WMIEFYAPWCPACQ..QPEWESFA
Retrocopy IAPSRSLAVPLAVLVLLLWGAPWTHWRQSNVHIITDENWRELLEGGWMIEFYAPWCPACQSHQPEWESFA

Parental  EWGEDL-EVNVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
          EWGEDL.EVNV.KVDVTEQPGL.G.F.ITALPTIYHCKDGEFR..QGPRTKKDFINFISDKEWKSIEPVS
Retrocopy EWGEDL<EVNVVKVDVTEQPGLTGQFTITALPTIYHCKDGEFRHPQGPRTKKDFINFISDKEWKSIEPVS

Parental  SWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
          SWFGPGSV.MSS.SALFQLSMWIRTCHNYFIEDLGLPVWGSY.VF.LATL..GLLLGLCMIFVADCLCPS
Retrocopy SWFGPGSVQMSSTSALFQLSMWIRTCHNYFIEDLGLPVWGSYAVFPLATLHCGLLLGLCMIFVADCLCPS

Parental  KRRRPQPYPHPSKKLLSESAQPLKKVEEEQEADEEDVSEEEAESKEGTNKDF-PQNAIRQRSLGPSLAAD
          .R.RPQPY..PSKKLLSESAQPLKK.EEEQEAD.EDVSEEEA.SKEGT.K.F.PQNAIRQ.SLGPSLA.D
Retrocopy ERHRPQPY--PSKKLLSESAQPLKKLEEEQEADKEDVSEEEAKSKEGT-KTF<PQNAIRQHSLGPSLATD

Parental  K
          K
Retrocopy K

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	5.25 RPM
SRP007412_cerebellum	2.31 RPM	6.57 RPM
SRP007412_heart	0.06 RPM	3.94 RPM
SRP007412_kidney	0.13 RPM	10.31 RPM
SRP007412_liver	0.24 RPM	8.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3058 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3058 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3840
Pan troglodytes	retro_ptro_2522
Gorilla gorilla	retro_ggor_2587
Macaca mulatta	retro_mmul_1618

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058 , retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,