RetrogeneDB ID: retro_lafr_79

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_111:3215248..3216121(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000026990
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCNY
• Ensembl ID: ENSLAFG00000012820
• Aliases: None
• Description: None

Sequence

>retro_lafr_79
GATCTGAACATGGAATTCAATCCTTCAGACCATCCTCGGGCCAGCACAATATTCCTCAGTAAATCTCAGACAGACGTGAG
AGAAAAACGCAAGAGTCTCTTCATTAACCATCATCCTCCAGGACAAGTAGCGAGGAAGTACAGCTCCTGCCCCACTATTT
TCCTAGATGATAGCACAGTCAGTCAGCCAAACCTCAAGTATACAATTAAATGTGTAGCTCTCGCAATATACTATCACATC
AAAAACAGGGACCCAGATGGAAGAATGCTCTTAGATATTTTTGATGAAAACCTTCACCCTCTTTCGAAATCCGAAGTGCC
ACCAGATTATGACAAACACAACCCAGAGCAGAAACAGATCTACCGGTTTGTTCGGACGCTGTTCAGTGCTGCCCAGCTGA
CGGCTGAATGTGCCATAGTCACCCTGGTATACCTTGAGAGACTTCTGACGTATGCAGAGATAGATATCTGTCCGGCAAAC
TGGAAGCGAATTGTCCTTGGGGCCATCTTGCTGGCCTCCAAAGTGTGGGACGACCAGGCGGTCTGGAATGTGGATTACTG
CCGGATCCTGAAAGACATCACCGTTGAAGACATGAATGAGCTAGAGCGACAGTTTCTTGAATTGCTCCAGTTCAACATCA
GCGTTCCTTCCAGTGTTTATGCCAAGTATTATTTTGATCTCCGTTCTCTGGCAGAAGCAAACAACCTGAGCTTCCCCTTG
GAGCCCCTCAGCAGGGAGAGGGCTCACAAGCTTGAGGCCATCTCTCGGCTGTGCGAGGACAAGTACAAGGACTTGAGAAC
ACCCACACGGAAGCGGTCAGCCAGTGCTGACAACCTAACTCTGACGCGGTGGTCCCCGGCCATCATCTCCTAA

Alignment

ORF - retro_lafr_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.62 %
• Parental protein coverage: 85.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQVARKYSSCSTIFLDDSTVSQPNLKYTIK
          DLNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQVARKYSSC.TIFLDDSTVSQPNLKYTIK
Retrocopy DLNMEFNPSDHPRASTIFLSKSQTDVREKRKSLFINHHPPGQVARKYSSCPTIFLDDSTVSQPNLKYTIK

Parental  CVALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIV
          CVALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIV
Retrocopy CVALAIYYHIKNRDPDGRMLLDIFDENLHPLSKSEVPPDYDKHNPEQKQIYRFVRTLFSAAQLTAECAIV

Parental  TLVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNELERQFLELLQ
          TLVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYC.ILKDITVEDMNELERQFLELLQ
Retrocopy TLVYLERLLTYAEIDICPANWKRIVLGAILLASKVWDDQAVWNVDYCRILKDITVEDMNELERQFLELLQ

Parental  FNINVPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDKYKDLRRPTRKRSASADNLT
          FNI.VPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDKYKDLR.PTRKRSASADNLT
Retrocopy FNISVPSSVYAKYYFDLRSLAEANNLSFPLEPLSRERAHKLEAISRLCEDKYKDLRTPTRKRSASADNLT

Parental  LTRWSPAIIS
          LTRWSPAIIS
Retrocopy LTRWSPAIIS

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_79 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006201	1 retrocopy	retro_chof_2504,
Echinops telfairi	ENSETEG00000005121	1 retrocopy	retro_etel_2021,
Loxodonta africana	ENSLAFG00000012820	1 retrocopy	retro_lafr_79 ,
Pan troglodytes	ENSPTRG00000002421	2 retrocopies	retro_ptro_1322, retro_ptro_3228,