RetrogeneDB ID: retro_lafr_795

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_39:13967181..13967764(+)
• Located in intron of: ENSLAFG00000017062

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSLAFG00000014743
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_lafr_795
ATGGGGTCTCAGACCTCCACATTACTGCAGGAGGAAGAGCTCGAGGAAGTCAAGCAGGAGACTGGCTTTTCCCACAATCA
GATTCATCCGAATCTATGGGCGGTTCACTAGTCTGGACTGAGGAGAGAATGGGACTCTCAGCTGGGAAGACTTCCAGCAG
ATTCCAGATCTTGTCATCAACCCATTGGGGGACCGTATCATCAGTGCCTTCTTTCCAGAAGGAGAGGACCAGGTCAACTT
CCGTGGATTCATAAGAACTTTGGCTTATTTCAGACCCACTGGCTGTAGTGAAGACAGCAAAGATGTGAATGGGCCAGAAC
CAATCAACAGCAGAATGAACAAACTGCACTTTGCTTTCAAATTATATGATTTGGATAAAGATGGCAAGATCTCCCATGAT
GAGCTGTTACAGGTGCTATGCATGATGGCTGGAGTGAATATCTTGGAAGAGCAGCTTGGGAGCATCACAGACAGGACCAT
CCAGGAGACCAATCTGGATGGGGATGGCGCCATATCTTTCTCAGAATTTGTTAAGGTTTTGGAAAAGGTTGACGTAGAAC
AGAGAATGAGCATTCACTTTCTT

Alignment

ORF - retro_lafr_795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQI-TRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINA
          MGS..STLL..EELEE.K.ETGFSH.QI..R.Y.RFTSLD.GENGTLS.EDFQ.IP.L.INPLGDRII.A
Retrocopy MGSQTSTLLQEEELEEVKQETGFSHNQI>IRIYGRFTSLD*GENGTLSWEDFQQIPDLVINPLGDRIISA

Parental  FFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVL
          FFPEGEDQVNFRGF.RTLA.FRP....E.SKDVNGPEP.NSR.NKLHFAF.LYDLDKD.KIS.DELLQVL
Retrocopy FFPEGEDQVNFRGFIRTLAYFRPTGCSEDSKDVNGPEPINSRMNKLHFAFKLYDLDKDGKISHDELLQVL

Parental  RMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFL
          .MM.GVNI..EQLGSI.DRTIQE...DGD.AISF.EFVKVLEKVDVEQ.MSI.FL
Retrocopy CMMAGVNILEEQLGSITDRTIQETNLDGDGAISFSEFVKVLEKVDVEQRMSIHFL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_795 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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	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,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
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,