RetrogeneDB ID: retro_lafr_938

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:51160967..51161237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUTA
• Ensembl ID: ENSLAFG00000005876
• Aliases: None
• Description: None

Sequence

>retro_lafr_938
TCCTCGGTGTCCCAGACCTTGCCAGCCTCAGTCTCTGGCTGTGTCCCCAGCTTGGTTTCAGGAGCCTTTGTCACCTGCTA
CAAAGAGAAGGCCACCAATGAGATTGCCAGGGCTGTGATGGAGAAGCACCTAGTAGCCTGCATCAGTCTCATCCCTCAGG
TTACATCCATCTGTGAGTGGAAGTGGACGATTCAGGAAGACAGTGAGGTGCCGATGATGATTAATGCCCAGAGTTCCTTG
GTTTCATATATGACCTGATTTGTTCGTTCA

Alignment

ORF - retro_lafr_938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPPSQPSPAPGSGYVPGSVSAAFVTCPNEKVAKEIARAVVEKRLAACVNLIPQITSIYEWKGKIEEDSEV
          S..SQ..PA..SG.VP..VS.AFVTC..EK...EIARAV.EK.L.AC..LIPQ.TSI.EWK..I.EDSEV
Retrocopy SSVSQTLPASVSGCVPSLVSGAFVTCYKEKATNEIARAVMEKHLVACISLIPQVTSICEWKWTIQEDSEV

Parental  LMMIKTQSSLVPALTDFVRS
          .MMI..QSSLV...T.FVRS
Retrocopy PMMINAQSSLVSYMT*FVRS

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_938 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
Loxodonta africana	ENSLAFG00000005876	1 retrocopy	retro_lafr_938 ,
Otolemur garnettii	ENSOGAG00000015556	1 retrocopy	retro_ogar_2719,