RetrogeneDB ID: retro_lafr_114

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:25151199..25151520(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000003419
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000017385
• Aliases: None
• Description: None

Sequence

>retro_lafr_114
ATGGTTAATGTACCTAAAACTCGAAGGACTTTCTGTAAGAAGTGTGGCAAGCATCAGCCTCACAAAGTGACCCAGTATAA
GAAGGGCAAGGATTCCTTGTATGCGCAGGGAAAGAGGCGCTATGATCGGAAGCAGAGCGGCTATGGCGGGCAGACAAAGC
CAATTTTTCGGAAGAAGGCGAAAACCACAAAGAAGATTGTGCTGAGGCTTGAATGTGTGGAGCCTAACTGCAGGTCCAAG
AGAATGCTGGCCATTAAGAGATGCAAGCATTTTGAGCTGGGAGGCGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTA
A

Alignment

ORF - retro_lafr_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE
          VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE
Retrocopy VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLE

Parental  CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
Retrocopy CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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_114 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Bos taurus	ENSBTAG00000019253	3 retrocopies	retro_btau_183, retro_btau_241, retro_btau_92,
Canis familiaris	ENSCAFG00000017688	1 retrocopy	retro_cfam_154,
Loxodonta africana	ENSLAFG00000017385	1 retrocopy	retro_lafr_114 ,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mustela putorius furo	ENSMPUG00000002168	3 retrocopies	retro_mputfur_269, retro_mputfur_530, retro_mputfur_94,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Tupaia belangeri	ENSTBEG00000015808	1 retrocopy	retro_tbel_52,