RetrogeneDB ID: retro_ggor_2587

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:40345083..40345909(-)
• Located in intron of: ENSGGOG00000006725

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSGGOG00000009768
• Aliases: None
• Description: None

Sequence

>retro_ggor_2587
ATGGCACCCTCCAGGAGTCTTGCAGTTCCGCTGGCAGTCCTGGTACTGTTGCTTGGGGGTGCTCCCTGGACCCACAGGCG
GCAGAGCAACGTACGCATCATCACAGACAAGAACTGGAGAGAGCTGCTGGAAGGAGGCTGGATGATACAATTTTATGCTC
CGTGGTGCCCTGCTTGTCAAAACCATTAACTGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTAAGGTTAATGTTG
TGAAAGTAGATGTCACAGAGCACCCAGGACTGACTGGACAGTTTACAATAACTGCTCTTCCTACTATTTATCATTGTAAA
GATGGTGAATTTAGGCATCCTCAGGGTCCAAGGACTAAGAAGGACTTCATAAACTTTATAAGTGATAAAGAGTGGAAGAG
TATTGAACCCGTTTCATCATGGTTTGGTTCAGGTTCTGTTCAGATGAGTAGTACGTCAGCACTCTTTCAGCTATCTACAT
GGATCAGGACTTGCCATAACTACTTTATTGAAGACATTGGATTGCCAGTGTGGGGATCATATGCTGTTTTTCCTTTAGCA
ACTGTGCATTCTGGACTGTTACTAGGACTCTGTATGATATTTGTGGCAGGTTGCCTTTGTCCTTCAGAAAGGCACAGACC
ACAGCCATACCCTTCAAAAAAATTATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACAAGAGGCGGATA
AAGAAGATGTTTCAGAAGAAGCAGCCAAAAGTAAAGAAGGAACAAAGACTTTCCACAGAATGCCATAAGACAACACTCTC
TGGGTCCATCACTGGTCACAGATAAA

Alignment

ORF - retro_ggor_2587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.7 %
• 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...EWESFA
Retrocopy MAPSRSLAVPLAVLVLLLGGAPWTHRRQSNVRIITDKNWRELLEGGWMIQFYAPWCPACQNH*LEWESFA

Parental  EWGEDL-EVNVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
          EWGEDL..VNV.KVDVTE.PGL.G.F.ITALPTIYHCKDGEFR..QGPRTKKDFINFISDKEWKSIEPVS
Retrocopy EWGEDL<KVNVVKVDVTEHPGLTGQFTITALPTIYHCKDGEFRHPQGPRTKKDFINFISDKEWKSIEPVS

Parental  SWFGPGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
          SWFG.GSV.MSS.SALFQLS.WIRTCHNYFIED.GLPVWGSY.VF.LAT..SGLLLGLCMIFVA.CLCPS
Retrocopy SWFGSGSVQMSSTSALFQLSTWIRTCHNYFIEDIGLPVWGSYAVFPLATVHSGLLLGLCMIFVAGCLCPS

Parental  KRRRPQPYPYLSKKLLSESAQPLKKVEEEQEADEEDVSEEEAESKEGTNKDF-PQNAIRQRSLGPSLATD
          .R.RPQPYP..SKKLLSESAQPLKK.EEEQEAD.EDVSEE.A.SKEGT.K.F.PQNAIRQ.SLGPSL.TD
Retrocopy ERHRPQPYP--SKKLLSESAQPLKKLEEEQEADKEDVSEEAAKSKEGT-KTF<PQNAIRQHSLGPSLVTD

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	0.82 RPM	10.79 RPM
SRP007412_cerebellum	1.50 RPM	9.46 RPM
SRP007412_heart	0.16 RPM	3.13 RPM
SRP007412_kidney	0.90 RPM	20.61 RPM
SRP007412_liver	1.42 RPM	15.51 RPM
SRP007412_testis	0.31 RPM	24.14 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2587 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3840
Pan troglodytes	retro_ptro_2522
Pongo abelii	retro_pabe_3058
Macaca mulatta	retro_mmul_1618

---

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,