RetrogeneDB ID: retro_lafr_244

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:38359574..38360060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HTATIP2
• Ensembl ID: ENSLAFG00000018703
• Aliases: None
• Description: None

Sequence

>retro_lafr_244
CCATTGATGACAGAGGAGCTACTCAAGCTTTGGGAAGACTTCAGGACGCAGAGTAAGTCCGTCTTTAGTCTGGGTACCAG
CGGGGAAACCGGAAAGTGCTCTTAAAAGAAATCCTGGAACAATGCCTGTTTTCCAAAGTCCCGCTCATTGGCTGAAGGAA
GCTCACCTTCGAGGAGGAAGCTTATAAAAATGTGAACCAAGAAGGGGTGGACTTTGAAAAGTTGGATGACTATGCACCTG
CCTTTCATGGTCGTGATGTAGGGTTCTGTTGCGCGGGTACCACCAGAACAAAAGTGGAGCCTAGGGATTTGTTCATGTTG
ATGGAGATTATGTGCTGAAGTCTGCAGAGCTGGCAAAAGCTGCAGGGTGCAAACATTTCAACTTGCTGTCCTCTAAAGGA
GCCGATAAGTCCAGCAATATTTTGTACCTGCAAATTAGGGAGAAGTGGAAGTCAGGGTTGAAGAATTAAAATTCGATGGT
TACTCC

Alignment

ORF - retro_lafr_244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 60.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSVTEMLPKLREDFRMQNKSVFILGASGETGK-VLLKEILEHNLFSKITLIGRRKLTFEEEAYKNVNQEV
          P..TE.L.KL.EDFR.Q.KSVF.LG.SGETGK.VLLKEILE..LFSK..LIG.RKLTFEEEAYKNVNQE.
Retrocopy PLMTEELLKLWEDFRTQSKSVFSLGTSGETGK<VLLKEILEQCLFSKVPLIG*RKLTFEEEAYKNVNQEG

Parental  VDFEKLDDYASVFQGHDVGFCCLGTTR-RKAGAEGFVRVDRDYVLKSAELAKAGGCKHFNLLSSKGADKS
          VDFEKLDDYA..F.G.DVGFCC.GTTR..K.GA.GFV.VD.DYVLKSAELAKA.GCKHFNLLSSKGADKS
Retrocopy VDFEKLDDYAPAFHGRDVGFCCAGTTR<NKSGA*GFVHVDGDYVLKSAELAKAAGCKHFNLLSSKGADKS

Parental  SNFLYLQIK-GEVEARVEELQFDRYS
          SN.LYLQI..GEVE.RVEEL.FD.YS
Retrocopy SNILYLQIR<GEVEVRVEELKFDGYS

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_244 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006718	1 retrocopy	retro_cjac_967,
Loxodonta africana	ENSLAFG00000018703	1 retrocopy	retro_lafr_244 ,
Oryctolagus cuniculus	ENSOCUG00000000749	1 retrocopy	retro_ocun_822,
Pongo abelii	ENSPPYG00000003421	1 retrocopy	retro_pabe_1288,
Ictidomys tridecemlineatus	ENSSTOG00000011216	2 retrocopies	retro_itri_1354, retro_itri_1523,