RetrogeneDB ID: retro_ocun_1947

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:93353800..93354218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MESDC2
• Ensembl ID: ENSOCUG00000016290
• Aliases: None
• Description: mesoderm development candidate 2 [Source:HGNC Symbol;Acc:13520]

Sequence

>retro_ocun_1947
CCCCCTACCCAGAAGAAGTAGTTCCACTACCACAATGATGTGGACATGGTATGTCTTCTTGTAGCAGTAGGTGAAAGATG
ATGGTATCAAAGAAGTAGATCTTCTAGAACAGAAAAGACCCTCAGAACCTGTTGATTTCTCAAAGATAGACCTGGGCAAT
CTTGAAAGCATATTAAAAATGATGAAGAAAGGGAAGATCCTTACGATGCTTTTCATTGTGTCAGGGAGCCCCACTGAGAA
GGGTATGGAGGAAATCATGAGCCCATGGCAAGGTAATCTTTTCAATGTCAAATACACTGTCCAGAGGTTCATTGTGGGAT
CACCCTGTGCTATCTTCATGCTTCATGATGGGGGAGGTATGCATGGGAGATCAAAGATTTTCTAGTCAGTTCCAGACAGG
TGTGTTCATGTTTCTCTG

Alignment

ORF - retro_ocun_1947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.2 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRKKKKDIRDYNDADMARLLE-QWEKDDDIEEGDLPEHKRPSAPVDFSKIDPGKPESILKMTKKGKTLMM
          P...KK.....ND.DM..LL..Q..KDD.I.E.DL.E.KRPS.PVDFSKID.G..ESILKM.KKGK.L.M
Retrocopy PPTQKK*FHYHNDVDMVCLLV>Q*VKDDGIKEVDLLEQKRPSEPVDFSKIDLGNLESILKMMKKGKILTM

Parental  FVTVSGSPTEKETEEITSLWQGSLFNANYDVQRFIVGSDRAIFMLRD-GG-YAWEIKDFLVSQ-DRCADV
          ...VSGSPTEK..EEI.S.WQG.LFN..Y.VQRFIVGS..AIFML.D.GG.YAWEIKDFLVS..DRC..V
Retrocopy LFIVSGSPTEKGMEEIMSPWQGNLFNVKYTVQRFIVGSPCAIFMLHDGGG<YAWEIKDFLVSS>DRCVHV

Parental  TL
          .L
Retrocopy SL

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	30.63 RPM
SRP017611_kidney	0.00 RPM	48.55 RPM
SRP017611_liver	0.00 RPM	18.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1947 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007811	1 retrocopy	retro_cjac_3285,
Homo sapiens	ENSG00000117899	1 retrocopy	retro_hsap_990,
Gorilla gorilla	ENSGGOG00000027583	1 retrocopy	retro_ggor_793,
Loxodonta africana	ENSLAFG00000014513	1 retrocopy	retro_lafr_505,
Monodelphis domestica	ENSMODG00000019402	2 retrocopies	retro_mdom_30, retro_mdom_344,
Oryctolagus cuniculus	ENSOCUG00000016290	1 retrocopy	retro_ocun_1947 ,
Pan troglodytes	ENSPTRG00000007366	1 retrocopy	retro_ptro_759,