RetrogeneDB ID: retro_ptro_2522

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:42614364..42615184(+)
• Located in intron of: ENSPTRG00000019106

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSPTRG00000006339
• Aliases: TMX1, TXNDC1
• Description: None

Sequence

>retro_ptro_2522
ATGGCACCCTCCAGGAGTCTTGCAGTTCCGCTGGCAGTCCTGGTACTGTTGCTTGGGGGTGCTCCCTGGACCCACAGGCG
GCAGAGCAACGTACGCATCATCACAGACAAGAACTGGAGAGAGCTGCTGGAAGGAGGCTGGATGATACAATTTTATGCCC
CGTGGTGCCCTGCTTGTCAAAACCATTAACCGGAATGGGAAAGTTTTGCTGAATGGGGAGATCTGAGGTTAATGTTGTGA
AAGTAGATGTCACAGAGCAGCCAGGACTGACTGGGCAGTTTACAATAACTGCTCTTCCTACTATTTATCATTGTAAAGAT
GGTGAATTTAGGCATCCTCAGGGTCCAAGGACTCAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAGTAT
TGAACCCGTTTCATCATGGTTTGGTTCAGGTTCTGTTCAGATGAGTAGTATGTCAGCACTCTTTCAGCTATCTACGTGGA
TCAGGACTTGCCATAACTACTTTATTGAAGACATTGGATTGCCAGTGTGGGGATCATATGCTGTTTTTCCTTTAGCAACT
CTGCATTCTGGACTGTTACTAGGACTCTGTATGATATTTGTGGCAGGTTGCCTTTGTCCTTCAGAAAGGCACAGACCACA
GCCATACCCTTAAAAAAAATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGCGGATAAAGAAG
ATGTTTCAGAAGAAGAAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAACACAACACTCTCTGGGTC
CATCACTGGTCACAGATAAA

Alignment

ORF - retro_ptro_2522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPSGSLAVPLAVLVLLLWGAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFA
          MAPS.SLAVPLAVLVLLL.GAPWTH.R.SNVR.ITD.NWRELLEG.WMI.FYAPWCPACQN..PEWESFA
Retrocopy MAPSRSLAVPLAVLVLLLGGAPWTHRRQSNVRIITDKNWRELLEGGWMIQFYAPWCPACQNH*PEWESFA

Parental  EWGEDL-EVNIAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
          EWG.DL.EVN..KVDVTEQPGL.G.F.ITALPTIYHCKDGEFR..QGPRT.KDFINFISDKEWKSIEPVS
Retrocopy EWG-DL<EVNVVKVDVTEQPGLTGQFTITALPTIYHCKDGEFRHPQGPRTQKDFINFISDKEWKSIEPVS

Parental  SWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
          SWFG.GSV.MSSMSALFQLS.WIRTCHNYFIED.GLPVWGSY.VF.LATL.SGLLLGLCMIFVA.CLCPS
Retrocopy SWFGSGSVQMSSMSALFQLSTWIRTCHNYFIEDIGLPVWGSYAVFPLATLHSGLLLGLCMIFVAGCLCPS

Parental  KKRRPQPYPYPSKKLLSESAQPLKKVEEEQEADEEDVSEEEAGSKEGTNKDF-PQNAIRQRSLGPTLATD
          ...RPQPYP......LSESAQPLKK.EEEQEAD.EDVSEEEA.SKEGT.K.F.PQNAI.Q.SLGP.L.TD
Retrocopy ERHRPQPYP---XXXLSESAQPLKKLEEEQEADKEDVSEEEAKSKEGT-KTF<PQNAITQHSLGPSLVTD

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	0.63 RPM	6.27 RPM
SRP007412_cerebellum	0.79 RPM	11.51 RPM
SRP007412_heart	0.20 RPM	9.21 RPM
SRP007412_kidney	0.92 RPM	22.60 RPM
SRP007412_liver	0.20 RPM	25.24 RPM
SRP007412_testis	0.21 RPM	17.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2522 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2522 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3840
Gorilla gorilla	retro_ggor_2587
Pongo abelii	retro_pabe_3058
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,