RetrogeneDB ID: retro_ocun_1444

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:33218662..33219065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CISD2
• Ensembl ID: ENSOCUG00000013943
• Aliases: None
• Description: CDGSH iron sulfur domain 2 [Source:HGNC Symbol;Acc:24212]

Sequence

>retro_ocun_1444
ATGGTGCTGGAGAGCGGGCCCGCATCGTGAAGGTGCAGCTCCCCACGGACCTGAAGTGGCTCCCGGTCCCGGAAAGCATT
ACCGGGTTTGCGTGGCTCACAGTTTCAGAATGGCTCCGGCTGCTGCCATTCCTTGTGAACTCGCACTGCTTGGCTACCTT
GCAGTTCAACCATTTTTCCCGAAGGAAAAACAACAGAAGGACAGCTTGATTAACCTTAAAATACAAAAGGAGAATCCGAA
AGTGGTAAATGAAATCAACATTGAAGATCTGGGCCTAACTAATGCAGCGAACTGTAGATGTTGGCGTCCTAAGACGTTTC
CTGCCTGTGATGGCTCACGTAATAAACACAATGAACTGACAGGAGATGATGTGGGTCCACTAATACTGAAGAAGAAAGAA
GTA

Alignment

ORF - retro_ocun_1444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVLESV-ARIVKVQLPAYLKRLPVPESITGFARLTVSEWLRLLPFLG-VLALLGYLAVRPFFPKKKQQKD
          MVLES..ARIVKVQLP..LK.LPVPESITGFA.LTVSEWLRLLPFL...LALLGYLAV.PFFPK.KQQKD
Retrocopy MVLESG<ARIVKVQLPTDLKWLPVPESITGFAWLTVSEWLRLLPFLV<ELALLGYLAVQPFFPKEKQQKD

Parental  SLINLKIQKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDGSHNKHNELTGDNVGPLILKKKEV
          SLINLKIQKENPKVVNEINIEDL.LT.AA.CRCWR.KTFPACDGS.NKHNELTGD.VGPLILKKKEV
Retrocopy SLINLKIQKENPKVVNEINIEDLGLTNAANCRCWRPKTFPACDGSRNKHNELTGDDVGPLILKKKEV

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	15.73 RPM
SRP017611_kidney	0.00 RPM	16.12 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1444 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1444 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010779	1 retrocopy	retro_cfam_1012,
Callithrix jacchus	ENSCJAG00000015530	1 retrocopy	retro_cjac_2668,
Felis catus	ENSFCAG00000028054	1 retrocopy	retro_fcat_1979,
Mus musculus	ENSMUSG00000028165	1 retrocopy	retro_mmus_2257,
Nomascus leucogenys	ENSNLEG00000026930	1 retrocopy	retro_nleu_1331,
Oryctolagus cuniculus	ENSOCUG00000013943	1 retrocopy	retro_ocun_1444 ,
Ictidomys tridecemlineatus	ENSSTOG00000001408	1 retrocopy	retro_itri_869,