RetrogeneDB ID: retro_lafr_752

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_35:4599152..4599581(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HEBP2
• Ensembl ID: ENSLAFG00000013501
• Aliases: None
• Description: None

Sequence

>retro_lafr_752
AAAACTGGCTTTACAAAAGTGAACAGCTACATTGAAGGCAAAAAGAAGAAAGAGATGAACATGAAGGTGACGGCTGCAGT
GACAAGCTTGGCGGAGCCAGGTTCAGGCCCTTTTAGTGAGTCTACCATCCCCATTCCCTGTAAGTCCCTTCTGAATGGCA
GTCTGATCTGCCCAAGCCTTCAGAGTCAGTTGTCTTCGTTGTAGACAGAGCCAAAATGACTGTGTTTGTACAGTCTTTCG
ATGAATTCTCTAGTGCCCAAAAGAATCAAGAACAACTTTTGACATTAGCAAACGTTTTGAGGGAAGAAGGAAAAATTTTC
AATGAAAAAGTTTACTACACCACTGGCTATAAAAGCCCTTTAAAATTGCTTAGTAGAAATAATAAAATGTGGCTGATTCA
GAAATAAAGAACCCTCCAAAGAAAATGAA

Alignment

ORF - retro_lafr_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 69.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTGFTKLNSYIEGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITI-SLYIPSGQQCDPPRPSESDVFIED
          .TGFTK.NSYIEGK..KEM..K.TA.VTS..EPGSGPFSESTI.I.SL..PS..Q.D.P.PSES.VF..D
Retrocopy KTGFTKVNSYIEGKKKKEMNMKVTAAVTSLAEPGSGPFSESTIPI<SL*VPSEWQSDLPKPSESVVFVVD

Parental  RAEMTVFVRSFDGFSSAQKNQEQLLTLANILREEGKVFDEKVYYTAGYNSPFKLLNRNNEVWLIQK-KER
          RA.MTVFV.SFD.FSSAQKNQEQLLTLAN.LREEGK.F.EKVYYT.GY.SP.KLL.RNN..WLIQK.KE.
Retrocopy RAKMTVFVQSFDEFSSAQKNQEQLLTLANVLREEGKIFNEKVYYTTGYKSPLKLLSRNNKMWLIQK>KEP

Parental  SKENE
          SKENE
Retrocopy SKENE

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_752 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019060	1 retrocopy	retro_cjac_2727,
Dasypus novemcinctus	ENSDNOG00000008868	1 retrocopy	retro_dnov_1268,
Echinops telfairi	ENSETEG00000009265	1 retrocopy	retro_etel_973,
Homo sapiens	ENSG00000051620	1 retrocopy	retro_hsap_2333,
Gorilla gorilla	ENSGGOG00000001584	1 retrocopy	retro_ggor_1770,
Loxodonta africana	ENSLAFG00000013501	1 retrocopy	retro_lafr_752 ,
Otolemur garnettii	ENSOGAG00000005010	1 retrocopy	retro_ogar_2762,