RetrogeneDB ID: retro_ocun_1396

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:4853031..4853481(+)
• Located in intron of: ENSOCUG00000009395

Retrocopy information

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

Parental gene information

• Parental gene symbol: GBAS
• Ensembl ID: ENSOCUG00000001768
• Aliases: None
• Description: glioblastoma amplified sequence [Source:HGNC Symbol;Acc:4179]

Sequence

>retro_ocun_1396
CGGAGATGGACATCTTCCAGTAACAGACCTCCAGAAGACAGCTGGTTAACACTCTTGTTTGTCTGCAAAGTTGATCCAAG
AAAAGTGCTCACTCCTGGCCAAAAAGCAAGAGCGGCCTTTACAATTTCGGTTTCACAATGCTAAACCAGAAGGCCTAGAT
GCATACAGTGAAGGTGGTCCACAGGTACTGCCAAGACTCACGAAGACAGCCACTGCCCTCGTGCTTTGGTGGGGACGTGG
AACACGTGGTACGAAGAGCAAGATGAAGCTGTCCACCTCTGCAGGTGTGACGGAGGCTCCCCAGCGCTCACAGAGGCCAT
GACTAAGCTCCGAGACGATCAGGAACTCCTGAGCTTCCGCAAGGCAAGAAGTGACGTGCTGCCGTCCAGGAGGAATCAGC
TGCTGTTGGAACTGCGTTTCGGGAATGAGCCGGTCCCGCGGTCAGGACCC

Alignment

ORF - retro_ocun_1396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.88 %
• Parental protein coverage: 55.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRLTSSNNRPREDSWLKSLFVRKVDPRK-DAHSNLLAKKETSSLY-KLQFHNVKPECLDAYNKICQEVLP
          RR.TSS.NRP.EDSWL..LFV.KVDPRK..AHS....K...S.LY....FHN.KPE.LDAY......VLP
Retrocopy RRWTSSSNRPPEDSWLTLLFVCKVDPRK<SAHSWPKSK---SGLY<QFRFHNAKPEGLDAYSEGGPQVLP

Parental  -KIHEDKHYPCTLVGTWNTWYGEQDQAVHLWRYEGGYPALTEVMNKLRENQEFVSFRKARSDMLLSRKNQ
          .K.HED.H.P..LVGTWNTWY.EQD.AVHL.R..GG.PALTE.M.KLR..QE..SFRKARSD.L.SR.NQ
Retrocopy <KTHEDSHCPRALVGTWNTWYEEQDEAVHLCRCDGGSPALTEAMTKLRDDQELLSFRKARSDVLPSRRNQ

Parental  LLLEFSFWNEPVPRSGP
          LLLE..F.NEPVPRSGP
Retrocopy LLLELRFGNEPVPRSGP

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	51.44 RPM
SRP017611_kidney	0.00 RPM	71.76 RPM
SRP017611_liver	0.00 RPM	78.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1396 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031598	1 retrocopy	retro_btau_361,
Macropus eugenii	ENSMEUG00000005152	2 retrocopies	retro_meug_1273, retro_meug_469,
Myotis lucifugus	ENSMLUG00000015038	1 retrocopy	retro_mluc_762,
Oryctolagus cuniculus	ENSOCUG00000001768	1 retrocopy	retro_ocun_1396 ,
Sarcophilus harrisii	ENSSHAG00000009627	1 retrocopy	retro_shar_473,
Tursiops truncatus	ENSTTRG00000015145	1 retrocopy	retro_ttru_1885,