RetrogeneDB ID: retro_ocun_1667

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018748:2045197..2045809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB14
• Ensembl ID: ENSOCUG00000013654
• Aliases: None
• Description: RAB14, member RAS oncogene family [Source:HGNC Symbol;Acc:16524]

Sequence

>retro_ocun_1667
GTCTTTAAATATACTATTATTGGGGACATGGGAATAAGAAAATCTTGCTTGCTTCATCAATTTACAGGAAAAAAAATTTG
TGGCTGATTGTCCTCACATAATTGGTGTTGAACTTGGTACAAGAAAAACTGAAGTTAGTGGCCAAACAAATCAAACTGCA
GATTTGGGATACAGTGGGACAGGGATGGTTTAGGGCTGTTCCATGAAGCTACTACAGAGGAGCTGCACACACACTTATGC
TGTGTGATACACTAGAAGAAGCACATATAATCACTTAAGCAGGTGTTTGACAGCTGTAAAGCATCTCATCATTCCAAACA
CTGGAATAATCCTAAGAGGAAATAAAGAAGATTTGGAAGGACAAAGAGATGTTACACATGAAGATGCCAAACACGGTGCT
GAAGCAAACAGCTTGCTGTTCTTGAAGCAAACACAAAAACGGGAGAGAATGTAGAAGGTCCTTTCCTTTAGGCTGCCAAA
AAAATCTATCAGAACATTCAGGACGGAAACCTGGATCTGAGTGCTGCCGAGTCTGCTGTCCAACACAAATCCTCAGCCAC
ACCCAGAAGCCAGGTGACTTGTGATCCCCAACCCCAGAGAGAAGGCTGTGGC

Alignment

ORF - retro_ocun_1667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.63 %
• Parental protein coverage: 94.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IFKYIIIGDMGVGKSCLLHQFT-EKKFMADCPHTIGVEFGTRIIEVSGQ-KIKLQIWDTAGQERFRAVTR
          .FKY.IIGDMG..KSCLLHQFT.EKKF.ADCPH.IGVE.GTR..EVSGQ..IKLQIWDT.GQ..FRAV..
Retrocopy VFKYTIIGDMGIRKSCLLHQFT>EKKFVADCPHIIGVELGTRKTEVSGQ>QIKLQIWDTVGQGWFRAVP*

Parental  SYYRGAAGALMVYDI-TRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYEEAKQFAEENG
          SYYRGAA..LM..D..TRRSTYNHLS..LT....L..PNT.IIL.GNK.DLE.QRDVT.E.AK..AE.N.
Retrocopy SYYRGAAHTLMLCDT<TRRSTYNHLSRCLTAVKHLIIPNTGIILRGNKEDLEGQRDVTHEDAKHGAEANS

Parental  LLFL-EASAKTGENVEDAFLEAAKKIYQNIQDGSLDLNAAESGVQHKPSAPQGGRLTSEPQPQREGCG
          LLFL.EA..KTGENVE..FL.AAKKIYQNIQDG.LDL.AAES.VQHK.SA......T..PQPQREGCG
Retrocopy LLFL<EANTKTGENVEGPFL*AAKKIYQNIQDGNLDLSAAESAVQHKSSATPRSQVTCDPQPQREGCG

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	61.87 RPM
SRP017611_kidney	0.00 RPM	51.79 RPM
SRP017611_liver	0.00 RPM	48.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1667 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081,
Myotis lucifugus	ENSMLUG00000009818	1 retrocopy	retro_mluc_1875,
Oryctolagus cuniculus	ENSOCUG00000013654	1 retrocopy	retro_ocun_1667 ,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Pelodiscus sinensis	ENSPSIG00000003919	1 retrocopy	retro_psin_66,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80,