RetrogeneDB ID: retro_lafr_422

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_152:686052..686901(-)
• 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_422
TGGTGCTGGGGTGTTGCTCTCCTGCCCAGGTCCTACACTGCCTGGGCTCTGGGGCATCTCGACCCACTGCTGCCACTGCT
ACTGCCACTGGTGATCTGGCATGGGGTAGGAGACAGCTGTTGTAATCCCTTAAGCATGGGTGCTGTTAAAAAAATGATTG
TGAAGAAAATACCTGCAATTTATGTCTTCTCTTTGGAGATTGGGAAGACACTGATATAGGATGTAGAGAACAGCTGCTTC
TTGAATGTCAATTTCCACGTATTGACAGTGTGTCAGACTCTCGCCATGGATCCTTAATTGTAGCAAGGCTATAATGCTAT
GGGATTCTCCCAGGGAGGCCAATTTCTGAGGGCAGTGGCTCAAAGATGCCCTCACCTCCCACAATCAATCTCATCTCTGT
TGAGGGACAGCATCAAGGTGTTTTTGGACTCCCTTGATGCCCAGGAGAGAGCTCTCCTGTCTGTGACTTGCTCAGGAAAA
TATTGAATGGTGGCGCTGCCTCCCAAAGCCATTCAAGAATGCCTGGTGCAAGCAGAATAGTGGCACGACCCCATAAAGGG
GGATGCATACTGCAACTATAGCATTTTCTTGTTGGATGTAAGTCAGGAGAGGGGTGTCAATGAGTCCTACAAGAAAAACC
TAATGACCTTGAAGAAGTTTGTGATGGTGAAATTCCTCAATGATCCCATTGTGGACCCTGTGGATTCCAAGTGCTTTGGA
TTTTACAAAAGTGGCCAAGCCAAGGAAACCATCCCCTTACAGAACACCGCTTTGTACATATTGGACAGCCTGGGTCTGAA
GGAAATGGGCAATGCAGGGAAGCCAGGCCTTCTGGCTACAGAAGGGGAC

Alignment

ORF - retro_lafr_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.49 %
• Parental protein coverage: 91.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLLAVILLPGFCAARALGHLDPPTPL--PLVIWHGMGDSCCNPFSMGAVKKMVERKIPGIYVLSLEIGKT
          W...V.LLP....A.ALGHLDP..PL..PLVIWHG.GDSCCNP.SMGAVKKM...KIP.IYV.SLEIGKT
Retrocopy WCWGVALLPRSYTAWALGHLDPLLPLLLPLVIWHGVGDSCCNPLSMGAVKKMIVKKIPAIYVFSLEIGKT

Parental  LTEDVENSFFLNVNSQVSTVCQTLAEDPRLQHGYNAMGFSQGGQFLRAVAQRCP-SPPMINLISVGGQQQ
          L..DVENS.FLNVN..V.TVCQTLA.DP.L..GYNAMGFSQGGQFLRAVAQRCP.SPP.INLISV.GQ.Q
Retrocopy LI*DVENSCFLNVNFHVLTVCQTLAMDP*L*QGYNAMGFSQGGQFLRAVAQRCP<SPPTINLISVEGQHQ

Parental  GVFGLPRCPGESSHICDLIRKTLNVGAYS-KAVQERLVQAEYWHDPIKEDTYRNHSIFLADINQERGVNE
          GVFGLP.CPGESS..CDL.RK.LN.GA.S.KA.QE.LVQAE.WHDPIK.D.Y.N.SIFL.D..QERGVNE
Retrocopy GVFGLP*CPGESSPVCDLLRKILNGGAAS>KAIQECLVQAE*WHDPIKGDAYCNYSIFLLDVSQERGVNE

Parental  SYKKNLMALKKFVMVKFLNDSIVDPVDSEWFGFYRSGQAKETIPLQKTTLYIQDRLGLKEMDKAGKLVFL
          SYKKNLM.LKKFVMVKFLND.IVDPVDS..FGFY.SGQAKETIPLQ.T.LYI.D.LGLKEM..AGK...L
Retrocopy SYKKNLMTLKKFVMVKFLNDPIVDPVDSKCFGFYKSGQAKETIPLQNTALYILDSLGLKEMGNAGKPGLL

Parental  AAEGD
          A.EGD
Retrocopy ATEGD

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_422 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,