RetrogeneDB ID: retro_lafr_930

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:71817524..71817842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C22ORF40
• Ensembl ID: ENSLAFG00000008671
• Aliases: None
• Description: None

Sequence

>retro_lafr_930
CCCCTGGGCATGTTCCAGCGCCAACTCTGTGTTCTGTCATCTCCATACAGCTACATGGAACAGAAGCCACCCAACATTTG
GCCTGTCGTCTTCCTGGAGGAGAGCTACATCTTCAAGGACTCTGTCACCACAGACAGAAACAATTTCCTGGCCCTTGGCG
CGTGTTACAGCAGATACAGCAGGCTGGTGTGTATGAGGGCCCGGAATGCAGTTTATTCTACTCCGAGATTTTGCCTCCCT
TATGTCTAAGACAACATTGATACCTTCCCACAGAAAGTTTGGCAAGAAGTGGAGAAGAGGAAAGCTCTGGCCAAGATG

Alignment

ORF - retro_lafr_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.49 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQGMFECQLCALSAPYSYVGQKPPDTRSVVLLEESYILKDPFTADRDKFLVLGSRCSVCSRLVCVGPECS
          P.GMF..QLC.LS.PYSY..QKPP....VV.LEESYI.KD..T.DR..FL.LG...S..SRLVC......
Retrocopy PLGMFQRQLCVLSSPYSYMEQKPPNIWPVVFLEESYIFKDSVTTDRNNFLALGACYSRYSRLVCMRARNA

Parental  LFYSKRFCLPCVRENIAAFPQEIRQDVEKRKALAKM
          .....RFCLP.V..NI..FPQ...Q.VEKRKALAKM
Retrocopy VYSTPRFCLPYV*DNIDTFPQKVWQEVEKRKALAKM

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_930 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002472	1 retrocopy	retro_etel_58,
Loxodonta africana	ENSLAFG00000008671	1 retrocopy	retro_lafr_930 ,