RetrogeneDB ID: retro_ocun_1044

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:66148337..66148995(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000029277
• Aliases: None
• Description: None

Sequence

>retro_ocun_1044
ATGGGGCTGTTTGGGAAAAGCCAGGAGAAGCCGCCCAAAGAGCTGGTCAATGAATGGTCACTGAAGATTAGAAAAGAAAT
GAGAAATGATAGGCAAATAAGAGACATACAAAGGGAAGAAGAAAAGGTGAAAGGATCTGTGAAGGATGCCGCCAAGAAGG
GCCAGAAGGATGTGTGTGTGGTTCTGGCCAAGGAAATGATCCGCTCCAGGAAGGCCGTGAGCAAGCTGTATGCGTCCAAA
GCCCACATGAACGCCGTCCTCGTGGGGATGAAGAACAGCTCGCGGTCCTGCGCGTGGCTGGTTCCCTGCAGAAGAGCACA
GAGGTGATGAAGGCCATGCAGAGCCTTGTGAAGATCCCAGAGATCCAGGCCACCATGAAGGAGCTGTCCAAGAGATGATG
AAGGCTGGGATCACAGAAGAAATGCTGGAGGACACTTTTGAAAGCATGGATGATCAGGAAGAAATGGAAGAGGCGGCAGA
GATGGAAATTGACAGAATTCTGCTTGAAACCACAGCAGGGGCCTTGGGCAAAGCGCCCAGTAAGGTGACCGACGCCCTGC
CGGAGCCCGAGCTCCCAGGAGCAATGGCTGCATCTGAAGACGACGAGGAGGAGGAAGCCCTGGAAGCCATGCAGTTGCTC
CTGGCCACACTCCGCAGC

Alignment

ORF - retro_ocun_1044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRS
          MGLFGK.QEKPPKELVNEWSLKIRKEMR..DRQIRDIQREEEKVK.SVKDAAKKGQKDVCVVLAKEMIRS
Retrocopy MGLFGKSQEKPPKELVNEWSLKIRKEMRN-DRQIRDIQREEEKVKGSVKDAAKKGQKDVCVVLAKEMIRS

Parental  RKAVSKLYASKAHMNSVLMGMKN-QLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSK-EMMKAG
          RKAVSKLYASKAHMN.VL.GMKN.QLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATM.ELSK.EMMKAG
Retrocopy RKAVSKLYASKAHMNAVLVGMKN<QLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMKELSK<EMMKAG

Parental  IIEEMLEDTFESMDDQEEMEEAAEMEIDRILFEITAGALGKAPSKVTDALPEPELPGAMAASEDEEEEEA
          I.EEMLEDTFESMDDQEEMEEAAEMEIDRIL.E.TAGALGKAPSKVTDALPEPELPGAMAASED.EEEEA
Retrocopy ITEEMLEDTFESMDDQEEMEEAAEMEIDRILLETTAGALGKAPSKVTDALPEPELPGAMAASEDDEEEEA

Parental  LEAMQSRLATLRS
          LEAMQ..LATLRS
Retrocopy LEAMQLLLATLRS

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	49.12 RPM
SRP017611_kidney	1.01 RPM	61.52 RPM
SRP017611_liver	0.00 RPM	9.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1044 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1044 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032, retro_cjac_2784,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044 ,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,