RetrogeneDB ID: retro_ecab_1099

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:12833679..12834260(-)
• Located in intron of: ENSECAG00000020766

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSECAG00000019751
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_ecab_1099
ATGGGGTCTCAGGCCTCGACGTTACTGCAGAAGGAAGAGCTCGAGGAAATCCAGTAGAAGACCCGCTTTTCCCACCACCA
GATCAACCAGCTTTACAGCCGGTTCACCAGCCTGGACAAAGGGGAGAACAGGGCCTTCAGCTAGGAAGATTTCCAGTGAA
TTCCAGAACTTGTCATCAATCCACTGGGGGACCAGCTCATCAGTGCCACCTTTCCAGAGGGAGAAGACCAAGTAAACTTC
CATGGAATCATAAAAACTTTGGCTCATTTCCAACCCACTGAAGATAATGCAAAGAGCAAAGATAAGACTGGACCAGAACC
ACTCAACAGCCAAAGCAACAAACTGTACGTTGTTTTTCAACTATGTGATTTGGATAAAGATGACAAGATCTCTTGCTGTG
AGTGTTCCAGGTGCTATGCAAGATGGTTGGAGTGAATATCTCAGATGAGCAACTGAGCAGCATCACAGACAGGACCATCC
AGGTGGCTGATCAGGAAGCGGATGATGCCCTATCTTTCGCAGAGTTTGTTAAGGTTTTGGAGAAGGTGGACGTAGAACAG
AAAATGAGCATCTGATTTCTT

Alignment

ORF - retro_ecab_1099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
          MGS.ASTLL..EELEEI...T.FSH.QI..LYSRFTSLDKGEN...S.EDFQ.IPEL.INPLGD..I.A.
Retrocopy MGSQASTLLQKEELEEIQ*KTRFSHHQINQLYSRFTSLDKGENRAFS*EDFQ*IPELVINPLGDQLISAT

Parental  FPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDE-LLQVL
          FPEGEDQVNF.G...TLAHF.P.EDN.KSKD..GPEPLNS.SNKL...F.L.DLDKDDKIS..E...QVL
Retrocopy FPEGEDQVNFHGIIKTLAHFQPTEDNAKSKDKTGPEPLNSQSNKLYVVFQLCDLDKDDKISCCE<VFQVL

Parental  RMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFL
          ..MVGVNISDEQL.SI.DRTIQ.ADQ..D.A.SF.EFVKVLEKVDVEQKMSI.FL
Retrocopy CKMVGVNISDEQLSSITDRTIQVADQEADDALSFAEFVKVLEKVDVEQKMSI*FL

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
SRP021940_articular_cartilage	0.00 RPM	45.16 RPM
SRP021940_cerebellum	0.00 RPM	41.34 RPM
SRP021940_embryo	0.10 RPM	31.15 RPM
SRP021940_placental_villous	0.05 RPM	30.60 RPM
SRP021940_synovial_membrane	0.05 RPM	20.59 RPM
SRP021940_testis	0.00 RPM	67.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1099 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1099 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1099 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_68
Bos taurus	retro_btau_1785
Canis familiaris	retro_cfam_2136

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 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	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
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,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
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,