RetrogeneDB ID: retro_lafr_697

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_30:27840584..27841490(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTDSS1
• Ensembl ID: ENSLAFG00000000061
• Aliases: None
• Description: None

Sequence

>retro_lafr_697
ACCATCACCTTTCTCAGGCTCATGTACTTCGCCTTCGCCAGGGATGATTCTGGTCCAGAAGACAACATCTGGAAGGGCAT
CCTCACTGTTATTTTCTTCCTTCTTATCATCAGTGTATTAGGTTTTCCCAAAGGTCCATTTACTAGGCCTCATCCAGCCT
TATGGAGAACGGTTTTTGGACTCAGTGTGCTCTGTTTCCTGTTCCTGGTCTTCCTCCTCTTCCTGAATTTCAAGCAGGTG
AAATCCATAATGTATTGGCTAGATCCAAATCTTCTCTATGCCACCAGGGAAGCAGATATCATGTAGTATGCCAGGAACTG
TCACGTTATCACCTGGGAGAGGATTATCAGCCACTTTGATATCTTTGCATTTGGGCATTTCTGGAGCTGTGCCATGAAGC
CCTTGCTGATCCATAGTTATGGCCTCTGCTGGACAATCAGTATTACCTGGGAGCTAACTGAGCTTTTCTTCATGCATCTT
CTGTCAAATTTTGCTGAGTGCTGGTGGGACCAAGTCATTCTGGACATCCTGCTATGTAATGGTGGTGGCATCTGGTTGGG
TATGGTTGTTTGCCGGTTCTTAGAAATGAGGACTTACCACTGGGCAAGCTTCAAGGACATTCACACCACCACCGGGAAAA
TCCAAAGAGCCATCCTGCAGTCCATCCCTGCTAGCTGGACCTATGTTCAGTGGTTTGACCCCAAATCTTCATTTCAGAGA
GTGGCTGGGATATACCCTTTCACTATCATCCAACAGCTGACTGAGTTGAGTACCTTCTTCTTGAAACATATGTTTATGTT
CCAAGCTAGCCATCCACTAAGTTGGTGCAGAATTCTCTTTATTGGTGGCATCACGGCTCCCACAGTGAGACAGTACGTAT
AATACTTACCTCATAGAACAGAGTGC

Alignment

ORF - retro_lafr_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFTIVSLMYFAFTRDDSGPEDNIWKGILSVIFFFLIISVLAFPNGPFTRPHPALWRMVFGLSVLYFLFLV
          ..T...LMYFAF.RDDSGPEDNIWKGIL.VIFF.LIISVL.FP.GPFTRPHPALWR.VFGLSVL.FLFLV
Retrocopy TITFLRLMYFAFARDDSGPEDNIWKGILTVIFFLLIISVLGFPKGPFTRPHPALWRTVFGLSVLCFLFLV

Parental  FLLFLNFEQVKSIMYWLDPNLRYATREADIMEYAVNCHVITWERILSHFDIFAFGHFWGWAMKALLIRSY
          FLLFLNF.QVKSIMYWLDPNL.YATREADIM.YA.NCHVITWERI.SHFDIFAFGHFW..AMK.LLI.SY
Retrocopy FLLFLNFKQVKSIMYWLDPNLLYATREADIM*YARNCHVITWERIISHFDIFAFGHFWSCAMKPLLIHSY

Parental  GLCWTISITWELTELFFMHLLPNFAECWWDQVILDILLCNGGGIWLGMVVCRFLEMRTYHWASFKDIHTT
          GLCWTISITWELTELFFMHLL.NFAECWWDQVILDILLCNGGGIWLGMVVCRFLEMRTYHWASFKDIHTT
Retrocopy GLCWTISITWELTELFFMHLLSNFAECWWDQVILDILLCNGGGIWLGMVVCRFLEMRTYHWASFKDIHTT

Parental  TGKIKRAVLQFTPASWTYVRWFDPKSSFQRVAGIYLFMIIWQLTELNTFFLKHIFVFQAGHPLSWCRILF
          TGKI.RA.LQ..PASWTYV.WFDPKSSFQRVAGIY.F.II.QLTEL.TFFLKH.F.FQA.HPLSWCRILF
Retrocopy TGKIQRAILQSIPASWTYVQWFDPKSSFQRVAGIYPFTIIQQLTELSTFFLKHMFMFQASHPLSWCRILF

Parental  IGGITAPTVRQYYAYLTD-TQC
          IGGITAPTVRQY..YL...T.C
Retrocopy IGGITAPTVRQYV*YLPHRTEC

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_697 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000000061	1 retrocopy	retro_lafr_697 ,