RetrogeneDB ID: retro_ocun_1213

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:135059897..135060395(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZB
• Ensembl ID: ENSOCUG00000014711
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, beta [Source:HGNC Symbol;Acc:1491]

Sequence

>retro_ocun_1213
TTAGAAGCCAACAATGCCTTTGACCAGTACCGAGACCTGTATTTTGAAGGTGGTGTCTCATCTGTCTACCTCTGGGATCT
GGGTCATGGCTTTGCGGGAGTGATCCTCATAAAGAAGGCTGGAGGTGGATCAAAGAAGATCAAAGGCTGCTGGGAGTCCA
TCCACGTGGTGGAAGTGCAGGAGAAGTCCAGTGGCCGCACCGCCCACTACAAGCTGACTTCCACGGTGATGCTGTGGCTG
CAGACCAACAAATCCGGCTCGGGTACCATGAACCTCGGAGGCAGCCTTACCAGACAGATGGAGAAAGATGAGACTGTGAG
TGACTGCTCCCCACACATAGCCAACATCGGGCGCCTGGTAGAGGACATGGAAAATAAAATCCGAAGTATGCTGAATGAGA
TCTACTTTGGGAAAACGAAGGACATCGTCAACGGGCTTAGGTCTGTGCAGACTTTTGCAGACAAATCTAAACAAGAAGCG
CTTAAGAACGACCTGGTA

Alignment

ORF - retro_ocun_1213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHY
          .EANNAFDQYRDLYFEGGVSSVYLWDL.HGFAGVILIKKAG.GSKKIKGCW.SIHVVEVQEKSSGRTAHY
Retrocopy LEANNAFDQYRDLYFEGGVSSVYLWDLGHGFAGVILIKKAGGGSKKIKGCWESIHVVEVQEKSSGRTAHY

Parental  KLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTK
          KLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRS.LNEIYFGKTK
Retrocopy KLTSTVMLWLQTNKSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSMLNEIYFGKTK

Parental  DIVNGLRSVQTFADKSKQEALKNDLV
          DIVNGLRSVQTFADKSKQEALKNDLV
Retrocopy DIVNGLRSVQTFADKSKQEALKNDLV

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	0.33 RPM	101.60 RPM
SRP017611_kidney	0.00 RPM	53.11 RPM
SRP017611_liver	0.08 RPM	29.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1213 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1213 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006715	1 retrocopy	retro_cjac_1184,
Dasypus novemcinctus	ENSDNOG00000018644	3 retrocopies	retro_dnov_1168, retro_dnov_1719, retro_dnov_2663,
Macropus eugenii	ENSMEUG00000002018	1 retrocopy	retro_meug_1958,
Myotis lucifugus	ENSMLUG00000012115	2 retrocopies	retro_mluc_1254, retro_mluc_2204,
Oryctolagus cuniculus	ENSOCUG00000014711	1 retrocopy	retro_ocun_1213 ,