RetrogeneDB ID: retro_lafr_144

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:87446169..87446595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000008585
• Aliases: None
• Description: None

Sequence

>retro_lafr_144
TGCTTGCAAAACCTTCTCAAGGCAGTGATGAAGCAGGTCGAAGAGGTCCTGCGCCAGCTGCATGCGCGGGACAAGGAGAA
GCAGCCTTGGGATATGCCGGAGACTCAGAATGCAGCCTCGCATCCCACACCGGAGCTGAGCCCTAGCGAGAGCCCCTGCC
CTTATTAGGCCTTCGCCAAAGTGAACAGAGTCAGCCTCCGCTTCCCTGCCAGCATCGCGGGTCTGCAGGTGGATAACGAG
ATTGTGCAGTTTGGCTCTGCAAATGCCCAGAACTTCCAGTGGCTGCAGAACGTGGGCAGTGTGGTGCAGCACAGCGAGGG
GAAGCCGCTGAATGCGACAGTGAACAGAAGAAAGGAAAGACCCCAGTTTAGGCTTGTCCCAACACGCTGGGCTGCAACGT
TATTCCTTTGCAAAAACGATTGTCCC

Alignment

ORF - retro_lafr_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.42 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLQNDHKAVMKQVEEALHQLHARDKEKQARDIAEAQNEAMSHRPDLSPSESPCPPRAFAKVNSISAGSPA
          CLQN..KAVMKQVEE.L.QLHARDKEKQ..D..E.QN.A....P.LSPSESPCP..AFAKVN..S...PA
Retrocopy CLQNLLKAVMKQVEEVLRQLHARDKEKQPWDMPETQNAASHPTPELSPSESPCPY*AFAKVNRVSLRFPA

Parental  SLAGLQVDDEIVEFGSVNTQNFQSLQNVGSVVQHSEGKPLNVTVIRRGERHQLRLVPTRWVGKGLLGCNI
          S.AGLQVD.EIV.FGS.N.QNFQ.LQNVGSVVQHSEGKPLN.TV.RR.ER.Q.RLVPTRW.....L..N.
Retrocopy SIAGLQVDNEIVQFGSANAQNFQWLQNVGSVVQHSEGKPLNATVNRRKERPQFRLVPTRWAATLFLCKND

Parental  VP
          .P
Retrocopy CP

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_144 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008038	1 retrocopy	retro_cfam_1020,
Loxodonta africana	ENSLAFG00000008585	1 retrocopy	retro_lafr_144 ,
Myotis lucifugus	ENSMLUG00000013501	1 retrocopy	retro_mluc_617,
Ochotona princeps	ENSOPRG00000016588	1 retrocopy	retro_opri_839,
Tursiops truncatus	ENSTTRG00000003021	1 retrocopy	retro_ttru_499,