RetrogeneDB ID: retro_ocun_841

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:67849187..67849666(-)
• Located in intron of: ENSOCUG00000021965

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB18
• Ensembl ID: ENSOCUG00000022307
• Aliases: None
• Description: RAB18, member RAS oncogene family [Source:HGNC Symbol;Acc:14244]

Sequence

>retro_ocun_841
ATGGACGAGGCCACGCCGACCACCCCGAGGAACCTCATCATCGGCCAGAATGGGGTGGGGAAGTCCAGCCTGCTCTTGGG
GCTCACAGATGATACCTCTGATCCAGAACTCACGGCCACAACAGGTGTGGAGTTGAAGGTGAAAACAATTTAGTGGATGG
AGATCAGGCTAAAGTTACAGTATGAGACAGTGCTGGGCAAGAGAGGTTTAGGACATCAACTGCTGGCTACTACAGAGGTG
CACTGCATGTATTTCAGTTTATGATGTCATGAGACAGGTTCACTCTTGTTAAACTGGGTAACTGGGTAAATTAGTTGGAA
ACTCACCATGTGAGAAGTGACATAGTAAACCTGCTTCTTGGAAATTAAATTCAAAAAGGAAAACAGGAAGTCCAGAGCCA
CGAAGGCCTGATATTTGCACAAAAGTAGTCTGTGTTATTTACAAAGGCAAGCGCAAATGCCTGTGACGGAGTCCAGTGT

Alignment

ORF - retro_ocun_841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.19 %
• Parental protein coverage: 77.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDEDVLTTLKILIIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTI-SVDGNKAKLAIWDTAGQER
          MDE...TT...LIIG..GVGKSSLLL..TDDT.DPEL.AT.GV..KVKTI..VDG..AK....D.AGQER
Retrocopy MDEATPTTPRNLIIGQNGVGKSSLLLGLTDDTSDPELTATTGVELKVKTI<LVDGDQAKVTV*DSAGQER

Parental  FRTLTPSYYRGAQGV-ILVYDVTR-RDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGL
          FRT.T..YYRGA..V.I.VYDV.R.R.T.VKL.NW.N.LET...R.DIVN.L.GN.I.K...EV...EGL
Retrocopy FRTSTAGYYRGALHV<ISVYDVMR>RFTLVKLGNWVN*LETHHVRSDIVNLLLGN*IQKGKQEVQSHEGL

Parental  KFARKHSMLFIEASAKTCDGVQC
          .FA.K.S.LF..ASA..CDGVQC
Retrocopy IFAQK*SVLFTKASANACDGVQC

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	0.11 RPM	31.95 RPM
SRP017611_kidney	0.00 RPM	31.62 RPM
SRP017611_liver	0.00 RPM	16.19 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_841 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_841 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633, retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841 ,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744, retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,