RetrogeneDB ID: retro_ocun_1274

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:34431374..34431950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CINP
• Ensembl ID: ENSOCUG00000026866
• Aliases: None
• Description: cyclin-dependent kinase 2 interacting protein [Source:HGNC Symbol;Acc:23789]

Sequence

>retro_ocun_1274
CAGACTGTTGGAATTATGACACTCAGAAAACCTGTTTTATCTGTCAGTGCAACAAAACTTAAGGAAAATGTAGCCAATTG
GCATAATTTTAATCCTGAAATCAGAAACCCTCAAAGATGCAGGCTTTACCACTACAAATGATATCACCAACCTAAAAATG
AGTTTATTGAATAAAGAAAAGATAGAATTAGAGAGCAGCAGCCCAGTTTCTAGTGAAAATGAAGAAAAGATGAATCTGAA
ATAAAATAAGGAGCTAAAGACAGTTCTATGAGGAACTGCAGGACACCTTGGCAGGTTTGAGCAAAATACAGGTGAAAATG
GAAAAGCTGTCTTCAACTACCAAGGAAATTTGTGAACAAGAAAATCACCATTATGAGGAGCAGTTGACTACTCCCTCTGT
TTCTCACATGGCCAACAGCCCATTTCTACAAGGTTTCCCGCAAGCTCTCTGATATGTACAGGCAGGAGCTGTTCCTGAAG
TGCACCCTGGCTGAAGAGCTGGCACACACCACAGACTGCGACCTCACCCTGAGCTACTTGTCAGTGTCGCTGCACTGGCC
TCACGTGACAGCAAGC

Alignment

ORF - retro_ocun_1274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 61.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KTLGITTPRKPVLSVSARKLKDNAADWHN-LILKWETLNDAGFTTANNIANLKISLLNKDKIELEGSSPA
          .T.GI.T.RKPVLSVSA.KLK.N.A.WHN.LILK.ETL.DAGFTT.N.I.NLK.SLLNK.KIELE.SSP.
Retrocopy QTVGIMTLRKPVLSVSATKLKENVANWHN>LILKSETLKDAGFTTTNDITNLKMSLLNKEKIELESSSPV

Parental  SSENGEKENVEYHKELEVLC-EELQATLDGLTKIQVKMEKLSSTTKGICELENYHYGEQSQRPP-MFHTW
          SSEN.EK.N....KEL.....EELQ.TL.GL.KIQVKMEKLSSTTK.ICE.EN.H..E.....P..F.TW
Retrocopy SSENEEKMNLK*NKELKTVL>EELQDTLAGLSKIQVKMEKLSSTTKEICEQEN-HHYEEQLTTP>LFLTW

Parental  PTAHFYEVSRKLSDMYRQELLLKRTVAEELAHTADRDLSLSYLSMWLHQPYVCST
          PTAHFY.VSRKLSDMYRQEL.LK.T.AEELAHT.D.DL.LSYLS..LH.P.V...
Retrocopy PTAHFYKVSRKLSDMYRQELFLKCTLAEELAHTTDCDLTLSYLSVSLHWPHVTAS

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	12.64 RPM
SRP017611_kidney	0.00 RPM	10.14 RPM
SRP017611_liver	0.08 RPM	3.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1274 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1274 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013323	1 retrocopy	retro_mdom_1091,
Oryctolagus cuniculus	ENSOCUG00000026866	1 retrocopy	retro_ocun_1274 ,
Otolemur garnettii	ENSOGAG00000009451	1 retrocopy	retro_ogar_321,
Sarcophilus harrisii	ENSSHAG00000007660	3 retrocopies	retro_shar_293, retro_shar_294, retro_shar_594,