RetrogeneDB ID: retro_ocun_1531

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02078537:25445..25899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSOCUG00000003591
• Aliases: None
• Description: F-actin-capping protein subunit alpha-2 [Source:UniProtKB/Swiss-Prot;Acc:Q09YN4]

Sequence

>retro_ocun_1531
AACAGACTTTGTTTCAAATTTGGTCACTTTAGAAAGTAAGTAACTGATCCAAGATCCAAGAAGCAGAAAATGTGATTGAT
CAGGGAGAAGGTCAGCAGAAACTGATCTTTGTGCTTATGTAAAAGAACATGATCCAAAGGGGGTCTGCACTGTATAGAGT
AAAAAGATAGATGGACAGCAAACCATTATTGCATGCATAGAAAACCATCAGTTTGAAGCAAAAAACTTTTGGAATGGCCC
CTGGAGATCAGAGAGGATGCTTTCAGTCACACCTTCAATTATTCAGGTTGTTGGTATCTTGACAATTCAGGTTCCTCACT
ATGAAGATGGTATTGTTCAGCTAGTGAGTCATAAAGATCTATTCCCCAATGAATCTAATGAGGCACAAATAGCAAAATAA
CTTACAAAAATTATATAAACTGTGAGAAATGAATACTAGACTGCTGTGAGTGAA

Alignment

ORF - retro_ocun_1531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.95 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NRICFKFDHLRKEATDPRP-YEAENAIE-SWRSSVETALRAYVKEHYPNGVCTVYGKKIDGQQTIIACIE
          NR.CFKF.H.RK..TDPR...EAEN.I..S.R.S.ET.L.AYVKEH.P.GVCTV..KKIDGQQTIIACIE
Retrocopy NRLCFKFGHFRK*VTDPRS<QEAENVID<SGRRSAETDLCAYVKEHDPKGVCTV*SKKIDGQQTIIACIE

Parental  SHQFQAKNFWNGRWRSEWKFTVTPSITQVVGILKIQVHYYEDGNVQLVSHKDIQDSLTVSNEAQTAKEFI
          .HQF.AKNFWNG.WRSE....VTPSI.QVVGIL.IQV..YEDG.VQLVSHKD.......SNEAQ.AK...
Retrocopy NHQFEAKNFWNGPWRSERMLSVTPSIIQVVGILTIQVPHYEDGIVQLVSHKDLFPN--ESNEAQIAK*LT

Parental  KIVEAAENEYQTAISE
          KI.....NEY.TA.SE
Retrocopy KII*TVRNEY*TAVSE

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	0.06 RPM	71.36 RPM
SRP017611_kidney	0.00 RPM	60.71 RPM
SRP017611_liver	0.00 RPM	12.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1531 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1531 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531 , retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,