RetrogeneDB ID: retro_ocun_844

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:81305582..81305823(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP4
• Ensembl ID: ENSOCUG00000015967
• Aliases: None
• Description: vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645]

Sequence

>retro_ocun_844
CCTTCCAAGTTCAAGGGTCACCTTAAATGATGATGATGATGCCACTGGTTCTGTGAAAAGTGAAAGGAAAAATCTTTTGG
AAGCTGATTCAGGTGAAGAAGAGGACTTTTTTCTAAGGGGACTGTCTGGACCAAGATTGGGACCTAGAAATGATAAAATT
AAGCATGTTCAGAATCAGATGGATGAAGTTACTGATGTCATGCAAGAAAATATTACACAGGTAATTGAAAGAGGGGACAG
G

Alignment

ORF - retro_ocun_844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKFKRH-LNDDD-VTGSVKSERRNLLEDDSDEEEDFFLRGPSGPRFGPRNDKIKHVQNQVDEVIDVMQE
          P.KFK.H.LNDDD..TGSVKSER.NLLE.DS.EEEDFFLRG.SGPR.GPRNDKIKHVQNQ.DEV.DVMQE
Retrocopy PSKFKGH>LNDDDDATGSVKSERKNLLEADSGEEEDFFLRGLSGPRLGPRNDKIKHVQNQMDEVTDVMQE

Parental  NITKVIERGER
          NIT.VIERG.R
Retrocopy NITQVIERGDR

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	25.61 RPM
SRP017611_kidney	0.00 RPM	10.54 RPM
SRP017611_liver	0.00 RPM	4.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_844 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016956	1 retrocopy	retro_amel_1457,
Felis catus	ENSFCAG00000013371	1 retrocopy	retro_fcat_1167,
Macropus eugenii	ENSMEUG00000011226	13 retrocopies	retro_meug_1053, retro_meug_115, retro_meug_1257, retro_meug_1406, retro_meug_1489, retro_meug_1587, retro_meug_163, retro_meug_2075, retro_meug_2154, retro_meug_319, retro_meug_386, retro_meug_569, retro_meug_75,
Monodelphis domestica	ENSMODG00000003811	1 retrocopy	retro_mdom_268,
Mustela putorius furo	ENSMPUG00000015609	1 retrocopy	retro_mputfur_315,
Oryctolagus cuniculus	ENSOCUG00000015967	1 retrocopy	retro_ocun_844 ,
Otolemur garnettii	ENSOGAG00000026745	1 retrocopy	retro_ogar_3369,
Pteropus vampyrus	ENSPVAG00000014342	1 retrocopy	retro_pvam_97,
Sarcophilus harrisii	ENSSHAG00000017179	2 retrocopies	retro_shar_584, retro_shar_747,
Vicugna pacos	ENSVPAG00000007424	1 retrocopy	retro_vpac_570,