RetrogeneDB ID: retro_hsap_3840

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:39608974..39609797(-)
• Located in intron of: ENSG00000241127

Retrocopy information

• Ensembl ID: ENSG00000236015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSG00000139921
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_hsap_3840
ATGGCACCCTCCAGGAGTCTTGCAGTTCCGCTGGCAGTCCTGGTACTGTTGCTTGGGGGTGCTCCCTGGACCCACAGGCG
GCAGAGCAACGTACGCATCATCACAGACAAGAACTGGAGAGAGCTGCTGGAAGGAGGCTGGATGATACAATTTTATGCCC
CGTGGTGCCCTGCTTGTCAAAACCATTAACCGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTGAGGTTAATGTTG
TGAAAGTAGATGTCACAGAGCAGCCAGGACTGACTGGACAGTTTACAATAACTGTTCTTCCTACTATTTATCATTGTAAA
GATGGTGAATTTAGGCATCCTCAGGGTCCAAGGACTCAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAG
TATTGAACCCGTTTCATCATGGTTTGTTTCAGGTTCTGTTCAGATGAGTAGTACGTCAGCACTCTTTCAGCTATCTACGT
GGATCAGGACTTGCCATAACTACTTTATTGAAGACATTGGATTGCCAGTGTGGGGATCATATGCTGTTTTTCCTTTAGCA
ACTCTGCATTCTGGACTGTTACTAGGACTCTGTATGATATTTGTGGCAGGTTGCCTTTGTCCTTCAGAAAGGCACACACC
ACAGCCATACCCTTCAAAAAAATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGCGGATAAAG
AAGATGTTTCAGAAGAAGAAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAACACAACACTCTCTGG
GTCCATCACTGGTCACAGATAAA

Alignment

ORF - retro_hsap_3840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.99 %
• 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
          EWGEDL.EVN..KVDVTEQPGL.G.F.IT.LPTIYHCKDGEFR..QGPRT.KDFINFISDKEWKSIEPVS
Retrocopy EWGEDL<EVNVVKVDVTEQPGLTGQFTITVLPTIYHCKDGEFRHPQGPRTQKDFINFISDKEWKSIEPVS

Parental  SWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
          SWF..GSV.MSS.SALFQLS.WIRTCHNYFIED.GLPVWGSY.VF.LATL.SGLLLGLCMIFVA.CLCPS
Retrocopy SWFVSGSVQMSSTSALFQLSTWIRTCHNYFIEDIGLPVWGSYAVFPLATLHSGLLLGLCMIFVAGCLCPS

Parental  KRRRPQPYPYPSKKLLSESAQPLKKVEEEQEADEEDVSEEEAESKEGTNKDF-PQNAIRQRSLGPSLATD
          .R..PQ..PYPSKKL.SESAQPLKK.EEEQEAD.EDVSEEEA.SKEGT.K.F.PQNAI.Q.SLGPSL.TD
Retrocopy ERHTPQ--PYPSKKL-SESAQPLKKLEEEQEADKEDVSEEEAKSKEGT-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
bodymap2_adipose	0.02 RPM	77.84 RPM
bodymap2_adrenal	1.23 RPM	66.24 RPM
bodymap2_brain	0.66 RPM	32.51 RPM
bodymap2_breast	0.12 RPM	68.29 RPM
bodymap2_colon	0.52 RPM	70.36 RPM
bodymap2_heart	0.13 RPM	18.85 RPM
bodymap2_kidney	0.39 RPM	74.10 RPM
bodymap2_liver	0.21 RPM	25.92 RPM
bodymap2_lung	0.25 RPM	47.35 RPM
bodymap2_lymph_node	1.08 RPM	67.45 RPM
bodymap2_ovary	0.87 RPM	61.92 RPM
bodymap2_prostate	0.45 RPM	53.81 RPM
bodymap2_skeletal_muscle	0.02 RPM	18.35 RPM
bodymap2_testis	0.21 RPM	68.25 RPM
bodymap2_thyroid	0.26 RPM	80.00 RPM
bodymap2_white_blood_cells	0.00 RPM	111.81 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3840 was not detected

EST

No EST(s) were mapped for retro_hsap_3840 retrocopy.

TSS

No TSS is located nearby retro_hsap_3840 retrocopy 5' end.

Lab

retro_hsap_3840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3840 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2522
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,