RetrogeneDB ID: retro_ocun_1470

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:34262643..34263371(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005941
• Aliases: None
• Description: None

Sequence

>retro_ocun_1470
GTCGCTGCCCACCTGCCGGCAGGAGTGACAACAAGAAGCAGGACCCTGTGCGCCATAGCCCTGTACCACATTGAAGAGTA
GGGCCAGCACCATTCTGAGAATTACTGCCTCTCCTTCAAGAATGTAGCTGGTCATTACATTTCCCCTTTTAATGATATTC
CTCTGAAAGGGGACTCTAGAGAAGGAAATGGCATTCCTACAAAGAGAGCACAACAGGATGAATATGCAAATTTGTTTAAC
ACGGTTGTACACGTACCTCTGTGGACAAATGCTAACGTGAGGATTCTCACCAAGGAGCCATTGGATCCCATTAAACAAGA
TGTAAAGCATGTATGCTGTGTGGCGAATATCTTGCCTCACCAAGGTTATATATGGAATTCTGATGCTCTCTCTCAGACTT
GGGAAGATCCCCATTAAACAGAGAAGAGCACAAACTGCTGTGGAGTTAATGATCCTATTGATGTTTGTGAAATAGGCTCA
AGGGTTATTCATGTGAAGAATCTTGGAATTTTGGCTCTGATTGATGAGGGTGAAATGGCTTAGAAATTAATTGCTATCAA
CATAAATGATCTACAAGCCTCAAAGTTTGATGATATTGATGATGTTAAGAAGTTCAAATCTGGTTACCTGGAAGCCATTC
TTTATTGGTTTAGATTTTAAAAAAGTACCAGATGAGAAAATCAGAAAACCAGTCTGTTTTTAATGGAGAACTCAGAAAAG
AGGCATAT

Alignment

ORF - retro_ocun_1470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 73.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAAHPPAGARARSGPLRAMALYHTEERGRPHSEDYRLFFKNVAGHYISPFHDIPLKVESKEENGIPTKKA
          VAAH.PAG...RS..L.A.ALYH.EE.G..HSE.Y.L.FKNVAGHYISPF.DIPLK..S.E.NGIPTK.A
Retrocopy VAAHLPAGVTTRSRTLCAIALYHIEE*GQHHSENYCLSFKNVAGHYISPFNDIPLKGDSREGNGIPTKRA

Parental  RNDEYENLFNMVVEVPRWTNAKMEIATKEPLNPIKQDVKHGKLRYVANIFPHKGYIWNYGALPQTWEDPH
          ..DEY.NLFN.VV.VP.WTNA...I.TKEPL.PIKQDVKH.....VANI.PH.GYIWN..AL.QTWEDPH
Retrocopy QQDEYANLFNTVVHVPLWTNANVRILTKEPLDPIKQDVKH--VCCVANILPHQGYIWNSDALSQTWEDPH

Parental  QTDESTNCCGDNDPIDVCEIGSKVLTRGEVVHVKILGILALIDEGETDWKLIAINANDPEASKFDDIDDV
          .T..STNCCG.NDPIDVCEIGS.V.....V....IL......DEGE...KLIAIN.ND..ASKFDDIDDV
Retrocopy *TEKSTNCCGVNDPIDVCEIGSRVI---HVKNLGILALI---DEGEMA*KLIAININDLQASKFDDIDDV

Parental  KKFKPGYLEATLNWFK-FYKVPD-GKPENQFAFNGEFRNKAF
          KKFK.GYLEA.L.WF..F.KVPD..K.ENQ..FNGE.R..A.
Retrocopy KKFKSGYLEAILYWFR>FKKVPD>RKSENQSVFNGELRKEAY

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	19.48 RPM
SRP017611_kidney	0.00 RPM	50.68 RPM
SRP017611_liver	0.00 RPM	4.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1470 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1470 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470 ,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,