RetrogeneDB ID: retro_ocun_1472

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:46590388..46591039(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSOCUG00000005362
• Aliases: None
• Description: cancer susceptibility candidate 4 [Source:HGNC Symbol;Acc:24892]

Sequence

>retro_ocun_1472
CTGCTGGGTTTCGAGGCCAACCCAAGGGCTGGCTGTCTGCCCTACTTTATGCTGGTGGTGCTTCTGGTAGTGATTGTTTT
CCTGGCGTTTACTACTAGAGCACTTCTTCCTGACACATCTTGCTTCCTGAGAAGAAGACTGAGCCACAGGGCCAGGTTCA
GTGCACAGAGATGGCCCGCAGGCATCTGAAGAAGTATAATTCAGATCTCTTGCTCTTGGTGGGCATGCATAAGAAACAGA
TGTACCAGAGGGGGCCAAATTATGGTCACCTCACCAGAAACCTGCTGGCTGGGAGGGTCTGGGGAAGAGATGCGAAGATG
ACAAGGTTAAACTACAGACCAGCATTTCATATCAGGTAGCAAACATCATTTAAAGGGGTAACTTGTTGAGCTTAATCAGG
AGTTTCTTCCACAAGAAGATCAGCTTCAACACTACAGACAGAAAAGTACTTTCCTTGTGAAGTGGTTAGCATATGAGAAT
TTTCAGTGTGGACAGCAGGTCAAGGAATTAAGAGCATGATTTGAAGAAAACTTAGCAGACCAATTTTTTCAACAAAAACA
AGAGACTCACAAAGTTCAAGCAAATGATGGAGAAAAATCAGCTGTGAATGATCATGTAGTAGCTAAAAATATTCCAAAAG
TAGCTGAGAAT

Alignment

ORF - retro_ocun_1472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVGFGANRRAGRLPSFVLVVLLVVIVVLAFN-YWSISSRHVLLQEEVAELQGQVQRTEVARGRLEKRNSD
          ..GF.AN.RAG.LP.F.LVVLLVVIV.LAF..Y.S.SS.H.LL.E...E.QGQVQ.TE.AR..L.K.NSD
Retrocopy LLGFEANPRAGCLPYFMLVVLLVVIVFLAFT<Y*STSS*HILLPEKKTEPQGQVQCTEMARRHLKKYNSD

Parental  LLLLVDTHKKQIDQKEADYGRLSSRLQAR-EGLGKRCEDDKVKLQNNISYQMADI-HHLKEQLAELRQEF
          LLLLV..HKKQ..Q....YG.L...L.A..EGLGKRCEDDKVKLQ..ISYQ.A.I.H.LK..L.EL.QEF
Retrocopy LLLLVGMHKKQMYQRGPNYGHLTRNLLAG<EGLGKRCEDDKVKLQTSISYQVANI<H-LKG*LVELNQEF

Parental  LRQEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQHEENIKKLADQFLQEQKQDAQKFQANDGEKLS
          L.QEDQLQ.YR...T.LVK.L.YE.FQCGQQ.KELRA..EEN...LADQF.Q.QKQ...K.QANDGEK..
Retrocopy LPQEDQLQHYRQKSTFLVKWLAYENFQCGQQVKELRA*FEEN---LADQFFQ-QKQETHKVQANDGEKSA

Parental  VNDHVVPKNIPEVAEN
          VNDHVV.KNIP.VAEN
Retrocopy VNDHVVAKNIPKVAEN

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	108.22 RPM
SRP017611_kidney	0.00 RPM	56.86 RPM
SRP017611_liver	0.00 RPM	37.30 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1472 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422, retro_chof_1445, retro_chof_2453, retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472 ,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852,