RetrogeneDB ID: retro_ocun_612

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:55401396..55401814(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000014484
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EFCAB2
• Ensembl ID: ENSOCUG00000029593
• Aliases: None
• Description: EF-hand calcium binding domain 2 [Source:HGNC Symbol;Acc:28166]

Sequence

>retro_ocun_612
GTAGCAGAATTGCACAAAAATATCAAAGAGGCGTTTGAAGTGTTGGACCGTGAGTCGAATAATACAGTGGATGGGAGGGA
GACTGGAACGACTGTCAGGTCCCTAGGGTGCTGCCCCAGTGAAGGTGAGCTCCACGAGCTGATTGCGGAGGTAGAGGAAG
AACCCGCTGGATACGTCCGATATGAAAGATTTCTTCCAGTGATGGCCAAAGCACTACTGGAAAAAAGGTACAGCCCAGTT
CCAGATGTTCTTCTTGGAGCTTCTGAGGCTTTAGATCCAGCTAAACGTGGGTTTCTTACTAAAGAACTGATCAAGTGTAT
GACTCGAAGAAGGTGAACCTTTTTCACTAGAGGAAATGGAAGAAATGTTGGCTGCTACAATTGATCCAGAAACAAATGCA
ATTCGTTACAAGGACTAT

Alignment

ORF - retro_ocun_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 90.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAELQKKIKEAFEVFDRESNNTVDVREIGTIVRSLGCCPSEGELHDLIAEVEEEEPTGYIRYEKFLPVMT
          VAEL.K.IKEAFEV.DRESNNTVD.RE.GT.VRSLGCCPSEGELH.LIAEV.EEEP.GY.RYE.FLPVM.
Retrocopy VAELHKNIKEAFEVLDRESNNTVDGRETGTTVRSLGCCPSEGELHELIAEV-EEEPAGYVRYERFLPVMA

Parental  KVLLEKRYRPIPEDVLLRAFEALDPAKRGFLTKEELIKYMT-EEGEPFSQEEMEEMLAATIDPETNAIHY
          K.LLEKRY.P.P.DVLL.A.EALDPAKRGFLTK.ELIK.MT.EEGEPFS.EEMEEMLAATIDPETNAI.Y
Retrocopy KALLEKRYSPVP-DVLLGASEALDPAKRGFLTK-ELIKCMT>EEGEPFSLEEMEEMLAATIDPETNAIRY

Parental  KDY
          KDY
Retrocopy KDY

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	0.17 RPM	4.75 RPM
SRP017611_kidney	0.20 RPM	3.45 RPM
SRP017611_liver	0.08 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_612 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029154	1 retrocopy	retro_cfam_781,
Callithrix jacchus	ENSCJAG00000016907	1 retrocopy	retro_cjac_3944,
Equus caballus	ENSECAG00000022403	1 retrocopy	retro_ecab_874,
Oryctolagus cuniculus	ENSOCUG00000007897	1 retrocopy	retro_ocun_180,
Oryctolagus cuniculus	ENSOCUG00000029593	1 retrocopy	retro_ocun_612 ,
Tarsius syrichta	ENSTSYG00000006254	2 retrocopies	retro_tsyr_1584, retro_tsyr_317,