RetrogeneDB ID: retro_ocun_1275

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:36830946..36831124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM32A
• Ensembl ID: ENSOCUG00000002238
• Aliases: None
• Description: family with sequence similarity 32, member A [Source:HGNC Symbol;Acc:24563]

Sequence

>retro_ocun_1275
TGTCTGGACAAGCGGCTCCCTCACCCAGGCAGCCTTCAAGAAGATGTAGGAGAAGCAGCAAATGGAAAGGATCCTGAAAA
AAGCATCTAAAACCCACCAACAGAGAGTGGTGGACTTCCACAGACATGTGGGTACACCCACAGAGCATTGCAACATTGCC
AACATCAGCCGGACAAAG

Alignment

ORF - retro_ocun_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 53.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CLDKRTP-AQAAFEKMQEKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK
          CLDKR.P..QAAF.KM.EK.QMERILKKASKTH.QRV.DF.RH..T.TEH..I...S.TK
Retrocopy CLDKRLP>TQAAFKKM*EKQQMERILKKASKTHQQRVVDFHRHVGTPTEHCNIANISRTK

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	48.68 RPM
SRP017611_kidney	0.00 RPM	43.08 RPM
SRP017611_liver	0.00 RPM	25.05 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1275 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1275 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017,
Oryctolagus cuniculus	ENSOCUG00000002238	1 retrocopy	retro_ocun_1275 ,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,