RetrogeneDB ID: retro_ocun_571

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:88875647..88876401(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSOCUG00000003980
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_ocun_571
ATGGTGCCCTCCAGGAGCCCAGTGCTTCCCCTGAGAGACTTGGTGTTGTTGCTTTGTGGGGTTCCCTACACCTACAGGCT
GCAGAGCAAGGTGTGCATCATCACCGAGAGCTGGAGAGAGTTGCTGGAAGGAGAGTGGATGGCAGAATTTTATGCTCCAA
GATGCTCTGCTTGTCAAATCCTCAACCAGATGGGAGCATTTTGCTGAATGGGAAGATTTTGAAGTGAATATTGGAAAAGC
AGATGTCACAGAGCAGACAGGACTGAGTGGATGGTCTATTATAATGGCTCTTCCTACTATTTACCATTGTAAAGATGGTG
AATTTAGGAGCTATCAGGGTCTGAGGACCAAGAAGGACTTCATAAACTTCCTAAGTGAGAAAGAGTGGAAGAGTATTGGG
CCTGTTTCGTCATAGTTTGGACCGCATTCTGTTCTGATGAGTAGTATGTCAGCACTCTCTCAGCTATCTATGTACATCAG
GACTTGTCATTACTACTTTATTGAAGACCTTGGGTTACCTGTTTGGGAATCATACACACTTTTGCTTCAGCAACTCTACT
TTCAGGATTGTTGTTAGGACTTTGCATGATATTTTGGGCAGATTGCCTTTCTTCTTCAAAACAATCAGACCACAGCCCTT
CCTTCAAAGAAATTATTGCCAGAATTTTCTTAGCCTTTGAAAAAAGTGGAAGAAGAACAAGAGCCTGATGAAGATGTTTC
AGAAAAGGAAGCCAAAAATGGAGGAAAAGCAAAG

Alignment

ORF - retro_ocun_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 91.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAPPGSPVLPLTVLVLLLWGAPCTYGRRSDVRVITDENWRELLEGEWMIEFYAPWCPACQ-NLQPE-WES
          M.P..SPVLPL..LVLLL.G.P.TY...S.V..IT.E.WRELLEGEWM.EFYAP.C.ACQ.N.QP..WE.
Retrocopy MVPSRSPVLPLRDLVLLLCGVPYTYRLQSKVCIIT-ESWRELLEGEWMAEFYAPRCSACQ<NPQPD<WEH

Parental  FAEWGEDLEVNVGKVDVTEQTGLSGRFIITALPTIYHCKDGEFRRYQGPRSKKDFINFISEKEWKSIEPV
          FAEW.ED.EVN.GK.DVTEQTGLSG..II.ALPTIYHCKDGEFR.YQG.R.KKDFINF.SEKEWKSI.PV
Retrocopy FAEW-EDFEVNIGKADVTEQTGLSGWSIIMALPTIYHCKDGEFRSYQGLRTKKDFINFLSEKEWKSIGPV

Parental  SSWFGPGSVLMSSMSALFQLSMYIRTCHNYFIEDLGLPVWGSYTV-FALATLLSGLLLGLCMIFLADCLC
          SS.FGP.SVLMSSMSAL.QLSMYIRTCH.YFIEDLGLPVW.SYT..FA.ATLLSGLLLGLCMIF.ADCL.
Retrocopy SS*FGPHSVLMSSMSALSQLSMYIRTCHYYFIEDLGLPVWESYTL<FASATLLSGLLLGLCMIFWADCLS

Parental  PSKRR-RPQPY-PSKKSLPEFSQPLKKVEEEQEADEEDVSEEEAKNGGGAK
          .SK...RPQP..PSKK.LPEFS.PLKKVEEEQE.D.EDVSE.EAKNGG.AK
Retrocopy SSKQS<RPQPF<PSKKLLPEFS*PLKKVEEEQEPD-EDVSEKEAKNGGKAK

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
SRP017611_brain	0.00 RPM	33.55 RPM
SRP017611_kidney	0.00 RPM	45.61 RPM
SRP017611_liver	0.00 RPM	19.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_571 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_571 has 0 orthologous retrocopies within eutheria group .

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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,