RetrogeneDB ID: retro_ocun_68

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:3633550..3634138(-)
• Located in intron of: ENSOCUG00000013436

Retrocopy information

• Ensembl ID: ENSOCUG00000028121
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSOCUG00000013832
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_ocun_68
ATGGGGTCTCAGGCCTCCACATTACTGCGGCATGAAGAGCTCGAGGAGATCAAGAAGGAGACTGGCTTTTCTCACAGTCA
GATTGCCCGACTCTACAAGCGGTTCACCAGCCTGGACGTAAATGGGGTTGGGGCTCTCAGCCGGGAAGATTTCCTGCGGA
TTCCAGAATTGGCCATCAACCCTCTGGGAGACCGGATCATCAGCGCCTTCTTTCCGGAGGGAGAAGATGAGGCCAACTTC
CGTGTATTCATAAGAATCTTGGCTCGTTTCCGACCCATCAGCGATAAGGAAAAGAGCAAAGATGCAAAGGGACCAGAGCC
ACTCAACAGCCGCAGCAACAAACTGCGTTTTGCTTTTCAACTGTATGATCTGGATAAAGATGACAAGATCTCCCGCAGTG
AGCTGATCCAGGTGTTACGCATGATGGTTGGAGTGAACATCTCGGAAGAGCAACTGGGCGTCATGGCCGACAGGACCATC
CAGGAGGCTGATGAGGACGGGGATGGTGCTATATCTTTCACAGAATTCGTTAAGGTTTTTGAGAAGACAGGCATAGAACA
GAAGATGAGCATCCAATTTCTTGACTAA

Alignment

ORF - retro_ocun_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.35 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVSASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFF
          G..ASTLLR.EELEEIKKETGFSHSQI.RLY.RFTSLD....G.LSREDF.RIPELAINPLGDRII.AFF
Retrocopy GSQASTLLRHEELEEIKKETGFSHSQIARLYKRFTSLDVNGVGALSREDFLRIPELAINPLGDRIISAFF

Parental  PEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRM
          PEGED..NFR.F.R.LA.FRPI.D.EKSKD..GPEPLNSRSNKL.FAF.LYDLDKDDKISR.EL.QVLRM
Retrocopy PEGEDEANFRVFIRILARFRPISDKEKSKDAKGPEPLNSRSNKLRFAFQLYDLDKDDKISRSELIQVLRM

Parental  MVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFL
          MVGVNIS.EQLG..ADRTIQEAD.DGD.AISFTEFVKV.EK...EQKMSI.FL
Retrocopy MVGVNISEEQLGVMADRTIQEADEDGDGAISFTEFVKVFEKTGIEQKMSIQFL

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	110.93 RPM
SRP017611_kidney	0.10 RPM	113.72 RPM
SRP017611_liver	0.00 RPM	20.96 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_68 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_68 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1785
Canis familiaris	retro_cfam_2136
Equus caballus	retro_ecab_1099

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Microcebus murinus	ENSMICG00000014362	1 retrocopy	retro_mmur_1556,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68 ,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,