RetrogeneDB ID: retro_mmul_1618

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:86677147..86677969(+)
• Located in intron of: ENSMMUG00000013563

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2213
• Ensembl ID: ENSMMUG00000001901
• Aliases: TMX1, TXNDC, TXNDC1
• Description: None

Sequence

>retro_mmul_1618
ATGGCACCTTCCAGGAGTCTTGTAGTTCCCCTGGCAGTCCTGGTACTGTTGCTTTGGGGTGCTTCCTGGACCCACAGGCA
GCAGAGCAACATACGTATCATCATGGACGAGAACTGGACAGAGCTGCTGGAAGGAGACTGGATGATAGAATTTTATGCCC
TGTGGTGCCCTGCTTGTCAAAACCTTCAACCGGAATGCGAAAGTTTTGCTGAATGGGGAGAATATCTGAGGTTAATGTTG
TGAAAGTAGATGTCACAGAGCAGTCAGGACTGACTGAACAGTTTACAATAACTGCTCTTCCTACTATTTATGATTGTAAA
GATAGTGAATTTAGGCACTTTCAGGGTCCAAGGACTAAGAAGGACTTCATAAACTTTTTAAGTGATAAACAGTGGAAGAG
TATTGAACCCATTTCATCATGGTTTGGTCCAGGTTCTGTTCAGATGAGTAGGATGTCAGCACTCTTTCAGCTATCTATGT
GGATCAGGACTTGCCATAACTACTTTATTGAAGACCTTGGATTGCCAGTGTGGGGATCATATACTGTTTTTCCTTTAGCA
ACTCTGCATTCTGGACTGTTATTAGAACTCTGTATGATATTTGTGGCAGATTGCCTTTGTCCTTCAAAAAGGCACAGACC
ACAGCTATACCCTTCAAAAAAATTATCAGAATCTGCTCAACCTTTGAAAAAACTGGAGGAAGAACGAGAGGCGGATGAAA
AAGATGTTTCAGAAGAAGCCAAAAGAAAAGAAGGAACAAAGATTTTCACAGAATGCCATAAGACAATGCTCTCTGGGTCC
ATCACTGGCCACAGATAAATCC

Alignment

ORF - retro_mmul_1618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPSGSPAVTLAVLVLLLWGAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFA
          MAPS.S..V.LAVLVLLLWGA.WTH...SN.R.I.DENW.ELLEGDWMIEFYA.WCPACQNLQPE.ESFA
Retrocopy MAPSRSLVVPLAVLVLLLWGASWTHRQQSNIRIIMDENWTELLEGDWMIEFYALWCPACQNLQPECESFA

Parental  EWGEDL-EVNVAKVDVTEQPGLSGRFIITALPTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVS
          EWGE.L.EVNV.KVDVTEQ.GL...F.ITALPTIY.CKD.EFR..QGPRTKKDFINF.SDK.WKSIEP.S
Retrocopy EWGEYL<EVNVVKVDVTEQSGLTEQFTITALPTIYDCKDSEFRHFQGPRTKKDFINFLSDKQWKSIEPIS

Parental  SWFGPGSVLMSSMSALFQLSMWIRACHNYFIEDLGLPVWGSYTVFALATLFSGLLLGLCMIFVADCLCPS
          SWFGPGSV.MS.MSALFQLSMWIR.CHNYFIEDLGLPVWGSYTVF.LATL.SGLLL.LCMIFVADCLCPS
Retrocopy SWFGPGSVQMSRMSALFQLSMWIRTCHNYFIEDLGLPVWGSYTVFPLATLHSGLLLELCMIFVADCLCPS

Parental  KRRRPQPYPYPSKKLLSESAQPLKKVEEEQEADEEDVSEEETER-KEGTNKDF-PQNAIRQRSLGPSLAT
          KR.RPQ.YP..SKKL.SESAQPLKK.E...E.........E....K...NKDF..QNAIRQ.SLGPSLAT
Retrocopy KRHRPQLYP--SKKL-SESAQPLKKLE--EEREADEKDVSEEAK<KKRRNKDF<SQNAIRQCSLGPSLAT

Parental  DKS
          DKS
Retrocopy DKS

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	1.90 RPM	11.77 RPM
SRP007412_brain_prefrontal_cortex	1.35 RPM	11.03 RPM
SRP007412_cerebellum	2.45 RPM	16.21 RPM
SRP007412_heart	0.94 RPM	9.95 RPM
SRP007412_kidney	1.53 RPM	20.07 RPM
SRP007412_liver	0.32 RPM	9.18 RPM
SRP007412_testis	0.60 RPM	8.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1618 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1618 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
Pongo abelii	retro_pabe_3058

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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,