RetrogeneDB ID: retro_ocun_962

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:3601088..3601666(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017863
• Aliases: None
• Description: None

Sequence

>retro_ocun_962
ATGGCTGCAGCCATTGCAAACTCACGTGTGAGTGCGGGGAAAAGGCTGAAAAATTCGCTAAAGAAGAAGAAGAAGGTGAA
AATGATTGCCAAAGTCATAGCATCAGAGCTGGAAGAGGAGGCAAAAGATGCTTCCGACAGTGGAGGATCTATAGGAAGCT
GTGGATCAGAAAAGGATCATTTTTCTGATGATGAAGCAACAGATGCTGACAATGAGGATGATGCTGAACCCTGTGACAAA
GAAAATGAAAATGCTGGAGAATCATGTGCTGGAACTAATATGGGCTGGGCAGATGCCATGGCTAAAATCCTCAACAAGAA
AACACCTAAAAGTAAACCCACCATTCTAGTCAAAAATAAAGAACTGGAAAAGGAAAAAGAAAAGTTAAAGCAAGAGAGAC
TTGAGAGAAGAAAACAGCTTGATAAGAGGTGGGAGTGGGAAATGATGTGCAGAGTAAAGCCAGATGTTGTCAAAGAAAAA
GAAGCAGAGAGAAATCTTCAGAGAATTGCAACGAGGGGTGTGGTGCAATTATTTATGCTGTCCAAAAACATCAAAAGAAT
GTTGATGAAAAGGTTAAA

Alignment

ORF - retro_ocun_962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 67.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVASSRVSAGKKLKNSLKKKKKVKMIAKVIASELEEEVKDASDSGGSIGSCGSEKGHFSDDEAIDAD
          MAAA.A.SRVSAGK.LKNSLKKKKKVKMIAKVIASELEEE.KDASDSGGSIGSCGSEK.HFSDDEA.DAD
Retrocopy MAAAIANSRVSAGKRLKNSLKKKKKVKMIAKVIASELEEEAKDASDSGGSIGSCGSEKDHFSDDEATDAD

Parental  NEDDAEPCDKENENAGESCAGTNMGWADAMAKILNKKTPKSKPTILVKNKELEKEKEKLKQERLERRKQL
          NEDDAEPCDKENENAGESCAGTNMGWADAMAKILNKKTPKSKPTILVKNKELEKEKEKLKQERLERRKQL
Retrocopy NEDDAEPCDKENENAGESCAGTNMGWADAMAKILNKKTPKSKPTILVKNKELEKEKEKLKQERLERRKQL

Parental  DKRREWEMMCRVKPDVVKDKEAERNLQRIATRGVVQLF-NAVQKHQKNVDEKVK
          DKR.EWEMMCRVKPDVVK.KEAERNLQRIATRGVVQLF..AVQKHQKNVDEKVK
Retrocopy DKRWEWEMMCRVKPDVVKEKEAERNLQRIATRGVVQLF<YAVQKHQKNVDEKVK

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	0.06 RPM	6.18 RPM
SRP017611_kidney	0.00 RPM	3.34 RPM
SRP017611_liver	0.00 RPM	1.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_962 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_962 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962 , retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,