RetrogeneDB ID: retro_ocun_800

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:50501911..50502276(+)
• Located in intron of: ENSOCUG00000029646

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1A
• Ensembl ID: ENSOCUG00000017003
• Aliases: None
• Description: RAB1A, member RAS oncogene family [Source:HGNC Symbol;Acc:9758]

Sequence

>retro_ocun_800
TTAGAGTTAGATGGGAAAGCAATCAAGCTTCAAATATGGGACACAGCAGGCTAATAAAGGTTTTGAACAATCACCTCCAG
TTATTACAGAGAACCCCATGGCGTCATAGCTGTGTACAATGTCACAGGTCAGGAGTCCTTCAATAGTCTTAAAGAGTGGC
TGCAGGAAATAGACCATCATGCCAATGAAAATGTCAACAACTTGGTGGTGGGAAACAAATGTGATCTGACCACAGTGAAA
GTAGTACATTACACAACAGCAAAGGAATTTGCCAATTCCCTTGAAATCCCATTCTTGGAAACAGTGCTAAGAACGCAACT
AATGTAGAACAGACTTTCCTAATGATGGCAGCTGAGATTAAAAAG

Alignment

ORF - retro_ocun_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.05 %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLV
          .ELDGK.IKLQIWDTAG..RF.TITSSYYR..HG.I.VY.VT.QESFN..K.WLQEID..A.ENVN.L.V
Retrocopy LELDGKAIKLQIWDTAG**RF*TITSSYYREPHGVIAVYNVTGQESFNSLKEWLQEIDHHANENVNNLVV

Parental  GNKCDLTTKKVVDYTTAKEFADSLGIPFLET-SAKNATNVEQSFMTMAAEIKK
          GNKCDLTT.KVV.YTTAKEFA.SL.IPFLET.SAKNATNVEQ.F..MAAEIKK
Retrocopy GNKCDLTTVKVVHYTTAKEFANSLEIPFLET<SAKNATNVEQTFLMMAAEIKK

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	160.98 RPM
SRP017611_kidney	0.00 RPM	194.00 RPM
SRP017611_liver	0.00 RPM	73.53 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_800 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_800 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800 ,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,