RetrogeneDB ID: retro_lafr_1090

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_68:10936173..10936716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1L4
• Ensembl ID: ENSLAFG00000012923
• Aliases: None
• Description: None

Sequence

>retro_lafr_1090
CCAGCCATGCCCCACCATAGGGCACTGCTCAACCTGTACTGGAATCCACAGAACATGGCTCAGACCACAGATGGATTACA
CTGTCATGTCAGCGACGTGGAAGCGCAGGAACACTATGATAACTTCTCTGAGGAGGTGTTCATAGAACTGCAGAAGAAAC
ATGGGGCGATTGAAGAGATGAATGTGTGCAACAACCTGGGAGACCATCTTGTAGGGAATGTCTGTGTCAAGTTCTGGTAG
GAGGAGGATGCAGAGCAGGCAGTGACTGAACTTAACAACCGCTGGTTCAATGGGCAGGCTGTGCATGCTGAGCTGTCTCC
TGTCACCGACTTCCGGGAGTTGTGCTGCTGACAGTACGAGACAGGGGAATGTACCTGTGGTGGCTTCCACAACTTTGTGC
ACCTGCAATCCATTTCCTGGAACCTCCAGTGGCAGCTGTATTGGCGGGGACCTTGGCGCAGTTCACCCTCAAGGACTCAT
ATGGGCCACCGTCCCCAAGAAAGGAACTGATGGTGTTCACTAGACCACTGGCATGGCTGCTTT

Alignment

ORF - retro_lafr_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 82.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTFSQTIVLLNLYRNPQNTAQTADGSHCHVSDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHL
          P.......LLNLY.NPQN.AQT.DG.HCHVSDVE.QEHYDNF.EEVF.ELQ.K.G.IEEMNVC.NLGDHL
Retrocopy PAMPHHRALLNLYWNPQNMAQTTDGLHCHVSDVEAQEHYDNFSEEVFIELQKKHGAIEEMNVCNNLGDHL

Parental  VGNVYVKFRREEDAERAVTELNNRWFNGQAVHAELSPVTDFRESCCRQYEMGECTRGGFCNFMHLRPISR
          VGNV.VKF..EEDAE.AVTELNNRWFNGQAVHAELSPVTDFRE.CC.QYE.GECT.GGF.NF.HL..IS.
Retrocopy VGNVCVKFW*EEDAEQAVTELNNRWFNGQAVHAELSPVTDFRELCC*QYETGECTCGGFHNFVHLQSISW

Parental  NLRRQLYGRGPRRRSPPRSHTGHRPRERNRRRSPDHRHGRF
          NL..QLY.RGP.R.SP.R.H.GHRP.ERN...S.DH.HG.F
Retrocopy NLQWQLYWRGPWRSSPSRTHMGHRPQERN*WCSLDHWHGCF

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_1090 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006383	1 retrocopy	retro_fcat_1650,
Gorilla gorilla	ENSGGOG00000016828	1 retrocopy	retro_ggor_150,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Loxodonta africana	ENSLAFG00000012923	1 retrocopy	retro_lafr_1090 ,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540,
Oryctolagus cuniculus	ENSOCUG00000013434	1 retrocopy	retro_ocun_1184,
Sus scrofa	ENSSSCG00000002896	1 retrocopy	retro_sscr_543,