RetrogeneDB ID: retro_ocun_1652

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018742:550642..551114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSOCUG00000009884
• Aliases: None
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_ocun_1652
GACGCTGAAGGTGATGTGGGAGTTCTCATGGGAGCATTGAGTTCAAGGAGAAGGAGTTGGACAGGGCTCAAGAACAACTG
GCCATGTTCTTACAGAAACTTGAGGGAGCAAAAAAGGCCACAGATGACAGCAATAGGGGAATGAAGGAGATAGAACACCA
GGCAGTGAAAGATGAGGAGATGGGGATTGAGGAGATACAGCTCAAATTGGTCAAGCACATTGCTGCGGAGGCTGATGGGA
AACACAGCGAGGTCACTCATAAACTGGTTATTCTGGAGCTCAGTTGGACAGAGCTCAGGAGCCAGTGGTGTCTGAACTAA
AATGTGTTGAACCACAGAAGGAGTCAGGGATGTTGCTGACAATCTGGGCTCACTCACGGCTGCTAACTGAAAAGTGTTCC
GAAGAAGAGGATGAATATTAAGAAGAAATTAAAATTATTTTTGACAAGCTGAAAGAGATTGATGCCTGTGCC

Alignment

ORF - retro_ocun_1652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DAEGDVAAL-NRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIENRAMKDEEKMEIQEMQL
          DAEGDV..L....I...E.ELDRAQE.LA..LQKLE.A.KA.D.S.RGMK.IE..A.KDEE.M.I.E.QL
Retrocopy DAEGDVGVL<HGSIEFKEKELDRAQEQLAMFLQKLEGAKKATDDSNRGMKEIEHQAVKDEE-MGIEEIQL

Parental  KEAKHIAEEADRKYEEVARKLVILE-GELERAEERAEVSELKCGDLEEE-LKNVTNNLKSLEAA-SEKYS
          K..KHIA.EAD.K..EV..KLVILE...L.RA.E...VSELKC.....E....V..NL.SL.AA..EK.S
Retrocopy KLVKHIAAEADGKHSEVTHKLVILE<AQLDRAQEPV-VSELKCVEPQKE<VRDVADNLGSLTAA>TEKCS

Parental  EKEDKYEEEIKLLSDKLKEAETRA
          E.ED.Y.EEIK...DKLKE....A
Retrocopy EEEDEY*EEIKIIFDKLKEIDACA

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	34.27 RPM
SRP017611_kidney	0.00 RPM	40.24 RPM
SRP017611_liver	0.00 RPM	23.20 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1652 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Homo sapiens	ENSG00000167460	2 retrocopies	retro_hsap_2623, retro_hsap_3969,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Oryctolagus cuniculus	ENSOCUG00000009884	1 retrocopy	retro_ocun_1652 ,
Oryctolagus cuniculus	ENSOCUG00000011821	2 retrocopies	retro_ocun_699, retro_ocun_8,