RetrogeneDB ID: retro_lafr_772

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_37:16254775..16255477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDFT1
• Ensembl ID: ENSLAFG00000007372
• Aliases: None
• Description: None

Sequence

>retro_lafr_772
CTGTTCTTGGCTTCTGAGTTAGAAGACTCTGTGCCTGGTGAAGATACAGAGCTTGCCAACTCTATGGGCCTGTTTCTGCA
GAAAATAAACATCAGTCGTAATTACCTGGAAGAAAAGCAAGAAGGAAGAGGGTTTGGGCCTCAAGAGGTTTGGAGCAGGT
ATGTTAAGAAGCTGGGTGATTTCACTAAACCACAAAATACTGACTTGGCTGTCCAGTGCCTGAATGAACTTACAGCCAAT
GCATTACACCACATCCCAGATGTCATCATCTACCTCTCAAGACTTAGAAACCAAAGTGTGTCTAACTCCTGTGCTGTTTC
ACATGTAATAGCCATAGTTCCTTTGGCTGCCTCTTCTAATGATCAATGGGTATTCAATGGCGTCATGAAGATCCCAAAAG
GGCAAGCAGTAACACTGATGGTGCATGCCACCAATATGCCAGCTATCCAAGCTATAATATAGCAGTATATGGAGGAAATT
TATCATAGAATCCCCGAATCAGACCCATCTTCTAATAAAACAAGGCAGTTCATCTCCACCATCAGGACACAGAATCTTCC
CACTTGTCAGCTGATCTCCCGAAGCCACTACTGTCCAATTTACCTGTCACTTGTTTTTGTCATACTCTTGGCTGCCTTGA
GCTGGCAGTATCTGCGCACACTATCCCAGGTCACAGAAGACTATGTTCAGACTGGAGAACAT

Alignment

ORF - retro_lafr_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 55.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFSASELEDSVVGEDTELANSMGLFLQKTNIIRDYLEDQQEGREFWPQEVWSRYVKKLSDFAKPENIDFA
          LF.ASELEDSV.GEDTELANSMGLFLQK.NI.R.YLE..QEGR.F.PQEVWSRYVKKL.DF.KP.N.D.A
Retrocopy LFLASELEDSVPGEDTELANSMGLFLQKINISRNYLEEKQEGRGFGPQEVWSRYVKKLGDFTKPQNTDLA

Parental  VQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAVPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLM
          VQCLNEL..NALHHIPDVI.YLSRLRNQSV.N.CAV..V.AI..LAA..N.Q.VF.GV.KI.KGQAVTLM
Retrocopy VQCLNELTANALHHIPDVIIYLSRLRNQSVSNSCAVSHVIAIVPLAASSNDQWVFNGVMKIPKGQAVTLM

Parental  MDATNMPAVKAIIYQYMEEIYHRIPKSDPSSNKTRQIISTIRQQNLPTCQLISRSHYSPIYLS--FVMLL
          ..ATNMPA..AII.QYMEEIYHRIP.SDPSSNKTRQ.ISTIR.QNLPTCQLISRSHY.PIYLS..FV.LL
Retrocopy VHATNMPAIQAII*QYMEEIYHRIPESDPSSNKTRQFISTIRTQNLPTCQLISRSHYCPIYLSLVFVILL

Parental  AALSWQYLSTLSQVTEDYVQTGEH
          AALSWQYL.TLSQVTEDYVQTGEH
Retrocopy AALSWQYLRTLSQVTEDYVQTGEH

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_772 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003988	2 retrocopies	retro_cjac_1945, retro_cjac_2761,
Erinaceus europaeus	ENSEEUG00000013655	1 retrocopy	retro_eeur_97,
Loxodonta africana	ENSLAFG00000007372	1 retrocopy	retro_lafr_772 ,
Mus musculus	ENSMUSG00000021273	1 retrocopy	retro_mmus_1182,
Vicugna pacos	ENSVPAG00000006183	1 retrocopy	retro_vpac_463,