RetrogeneDB ID: retro_ocun_1532

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02078537:40057..41111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX3
• Ensembl ID: ENSOCUG00000005000
• Aliases: None
• Description: thioredoxin-related transmembrane protein 3 [Source:HGNC Symbol;Acc:24718]

Sequence

>retro_ocun_1532
TTAAAGGGGGATTTGGCATATAATTACAGAGGACCACGAACTAAAGATGATATTATTGAATTTGCTCACAGAGTATCTGG
GGCTTTAATTCGGCCACTTCCAAGTCAGCAAATGTTTGAACATGTACAGAAGAGACATCGTGTATTTTTCGTTTACATAG
GTGGAGAATCACCTTTGAAAGAGAAATACATCGATGCTGCTTCAGAATTGATTGTATATACATACTTTTTTTCTGCCCCT
GAAGAAGTAGTTCCTGAGTATGTGACACTGAAAGAGATGCCTGCTGTGCTTGTTTTCAAAGATGAAACCTACTTTGTTTA
TGATTAGTATGAAGATGGTGATCTGTCATCATGGATCAACCGGGAGAGATTTCAGAATTACCTTACTGTGGATGGCTTCA
TTTTGTATGAACTTGGAGATACAGGAAAGCTCGTGGCTATTGCAGTTATTGATGAGAAAAATACATCACATGAGCATACC
AGATTAAAGTCAATTATTCAGGAAGTTGCTAGAGATTACAGAGACCACTTCCATAGGGATTTTCAGTTTGGCCACATGGA
TGGAAATGACTATATAAATACCCTGCTGATGGAGTGATGAATTGGCAGTGCCAACCGTGGTTGTACTGAATACTTCAAAC
CAGCAATACTTTTTGCTAGACAGACAGATTAAGGATACCAAAGACATGGTCCAATTCATTAATAACATTCTGGATGGCAC
AGTAGAGGCCCAAGGAGGTGATAGCATTTTCCAGAGATTGAAGAGAATAGTATTTGATGCCAAATCTACCTTAGTGTCTA
TATTCAAGAGCTCCCCGCTCATGGGCTGCTTCCTCTTTGGCCTGCCACTGGGTGTCATCAGTATCATGTGCTATGGGATC
TACACAGCGGACACTGATGGGGGTTACGTGGAGGAACGGTATGAAATATCAAAAAGTGAAGATGAAAGCCAAGAACAGAT
AGAAGAAAACAAAGAACAGCAGGAGCCAAGCAGTGGAGGCTCTTTAGTGTCTACTGAACAAGAGCCCAAGGATGTGTTAG
AAAAGAAGAAAGAT

Alignment

ORF - retro_ocun_1532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKGDLAYNYRGPRTKDDIIEFAHRVSGALIRPLPSQQMFEHVQKRHRVFFVYIGGESPLKEKYIDAASEL
          LKGDLAYNYRGPRTKDDIIEFAHRVSGALIRPLPSQQMFEHVQKRHRVFFVYIGGESPLKEKYIDAASEL
Retrocopy LKGDLAYNYRGPRTKDDIIEFAHRVSGALIRPLPSQQMFEHVQKRHRVFFVYIGGESPLKEKYIDAASEL

Parental  IVYTYFFSAPEEVVPEYVTLKEMPAVLVFKDETYFVYDEYEDGDLSSWINRERFQNYLTVDGFLLYELGD
          IVYTYFFSAPEEVVPEYVTLKEMPAVLVFKDETYFVYD.YEDGDLSSWINRERFQNYLTVDGF.LYELGD
Retrocopy IVYTYFFSAPEEVVPEYVTLKEMPAVLVFKDETYFVYD*YEDGDLSSWINRERFQNYLTVDGFILYELGD

Parental  TGKLVAIAVIDEKNTSLEHTRLKSIIQEVARDYRDHFHRDFQFGHMDGNDYINTLLMD-ELAVPTVVVLN
          TGKLVAIAVIDEKNTS.EHTRLKSIIQEVARDYRDHFHRDFQFGHMDGNDYINTLLM.........VV..
Retrocopy TGKLVAIAVIDEKNTSHEHTRLKSIIQEVARDYRDHFHRDFQFGHMDGNDYINTLLME>DELAVPTVVVL

Parental  TSNQQ-YFLLDRQIKDTKDMVQFINNILDGTVEAQGGDSIFQRLKRIVFDAKSTIVSLYSRASPLMGCFL
          ....Q.YFLLDRQIKDTKDMVQFINNILDGTVEAQGGDSIFQRLKRIVFDAKST.VS.....SPLMGCFL
Retrocopy NTSNQQYFLLDRQIKDTKDMVQFINNILDGTVEAQGGDSIFQRLKRIVFDAKSTLVSIF-KSSPLMGCFL

Parental  FGLPLGVISIMCYGIYTADTDGGYVEERYEISKSEDESQEQIEENKEQQEPSSGGSLVPTEQEPKDVLEK
          FGLPLGVISIMCYGIYTADTDGGYVEERYEISKSEDESQEQIEENKEQQEPSSGGSLV.TEQEPKDVLEK
Retrocopy FGLPLGVISIMCYGIYTADTDGGYVEERYEISKSEDESQEQIEENKEQQEPSSGGSLVSTEQEPKDVLEK

Parental  KKD
          KKD
Retrocopy KKD

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	0.39 RPM	24.83 RPM
SRP017611_kidney	0.30 RPM	9.83 RPM
SRP017611_liver	0.15 RPM	2.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1532 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005000	2 retrocopies	retro_ocun_1532 , retro_ocun_1820,