RetrogeneDB ID: retro_lafr_199

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:14902582..14903348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPT1
• Ensembl ID: ENSLAFG00000022663
• Aliases: None
• Description: None

Sequence

>retro_lafr_199
ATGGGTGCTGTTAAAAAATGGTTGAGAAGAAATTTATGGAATGTATGTCTTTCCTTTGGAGATTGAGAAGATGCTAACAG
AGGATGTGAAGAACAGCTTCTTCTTGAATGTCAATTCCCAAGTATCCACAGTGTGTCAGACTCTTGCTGAAGATCCTAAA
TTTCAGCAAGGCTACAATGCTATGGCGTTCTCTCAGGGAGACCAATTTCTGAGGACAGGGGCTCAGAGATGCCCATCACC
TCCTATACTCAATTTCATCTCCATTGGGGGAAAACAGCAAGGTATTTTTCAACTCCCTCAATGCCTAGGAGAGAGCTCTC
ACATCTGTGACTTGATCAGGAAAACATTAAATGTTGGGGCTTATTGCAAAGCCATTCAAGAATGCCTGGTGCAAGCAGAA
TGCTGGCACGACCCCATAAAGGAGGACGTGTACTGCCACCACAGCACCTTCTGGGCAGATGTAAATCAGGAGAGGGGTGT
CAATGAGTCCTACAAGAAAAACCTGACTGCCTTGAAGAAGTTTGTGATGGTGAAATTCCTCAATGCTTCCATTGTGGATA
CTGTGGATTCTGAGTGGTTTGGATTTTACCGAAGTGACCAAGCCAAGGAAACCATCTCCTTGCAGAAGACCACTCTGCAC
ATGCAGGACCACCTGGGGCTAAAGGAAATGGACAGTGCAGCGAAGCTAGTCTTCCTGGCTACAGAAGGAGACCATCTTCA
TCTGTCTAAAGAATAGCATGATGCCCACATCATTCCCTTCCTTAAA

Alignment

ORF - retro_lafr_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 83.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGAVKK-MVERK-IPGIYVLSLEIGKTLTEDVENSFFLNVNSQVSTVCQTLAEDPRLQHGYNAMGFSQGG
          MGAVKK.MVE.K.I.G.YV..LEI.K.LTEDV.NSFFLNVNSQVSTVCQTLAEDP..Q.GYNAM.FSQG.
Retrocopy MGAVKK<MVEKK<IYGMYVFPLEIEKMLTEDVKNSFFLNVNSQVSTVCQTLAEDPKFQQGYNAMAFSQGD

Parental  QFLRAVAQRCPSPPMINLISVGGQQQGVFGLPRCPGESSHICDLIRKTLNVGAYSKAVQERLVQAEYWHD
          QFLR..AQRCPSPP..N.IS.GG.QQG.F.LP.C.GESSHICDLIRKTLNVGAY.KA.QE.LVQAE.WHD
Retrocopy QFLRTGAQRCPSPPILNFISIGGKQQGIFQLPQCLGESSHICDLIRKTLNVGAYCKAIQECLVQAECWHD

Parental  PIKEDTYRNHSIFLADINQERGVNESYKKNLMALKKFVMVKFLNDSIVDPVDSEWFGFYRSGQAKETIPL
          PIKED.Y..HS.F.AD.NQERGVNESYKKNL.ALKKFVMVKFLN.SIVD.VDSEWFGFYRS.QAKETI.L
Retrocopy PIKEDVYCHHSTFWADVNQERGVNESYKKNLTALKKFVMVKFLNASIVDTVDSEWFGFYRSDQAKETISL

Parental  QKTTLYIQDRLGLKEMDKAGKLVFLAAEGDHLQLSEEWFDAHIIPLLQ
          QKTTL..QD.LGLKEMD.A.KLVFLA.EGDHL.LS.E..DAHIIP.L.
Retrocopy QKTTLHMQDHLGLKEMDSAAKLVFLATEGDHLHLSKE*HDAHIIPFLK

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_199 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
Bos taurus	ENSBTAG00000013367	1 retrocopy	retro_btau_348,
Canis familiaris	ENSCAFG00000003004	1 retrocopy	retro_cfam_1985,
Loxodonta africana	ENSLAFG00000022663	2 retrocopies	retro_lafr_199 , retro_lafr_422,
Procavia capensis	ENSPCAG00000002429	1 retrocopy	retro_pcap_94,
Tursiops truncatus	ENSTTRG00000004339	1 retrocopy	retro_ttru_659,