RetrogeneDB ID: retro_lafr_777

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_38:4945345..4945680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000015020
• Aliases: None
• Description: None

Sequence

>retro_lafr_777
TTGGTAGGTGGCCTCATGGACAAGGATGTGAATGAGTGGGACTGCAGGGTGTGCTAGACTTTTCCCTCAGCGAGTACAAC
AAGGCGAGCAGTGGCAAGTTCCACAGCCATGTGGTGCAGGTGGTGCAGGCCTGCAAGCATATCATGTCTGGGGTGAACTA
ATTCTTGGACGTGGAGATTAGACAAACCACATGTACTGAGTCCTACCTCAACTTAGCCACCTATCCCTTCCATGACCAGC
CACACCCGAGGAAGAAAGCCCTCTGCTCTTTTAATATATATACTGTTCCTTGGCTGGGCACAACCTCCATGATGAAATCC
AACTGCCAGAACGCA

Alignment

ORF - retro_lafr_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 85.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLGGIMDADENE-EGVQRALDFAISEYNKASNDKFHSRVVQVVRARKQIVSGVNYFLDVEIGRTTCTKSQ
          L.GG.MD.D.NE..G.Q..LDF..SEYNKAS..KFHS.VVQVV.A.K.I.SGVN.FLDVEI..TTCT.S.
Retrocopy LVGGLMDKDVNE<VGLQGVLDFSLSEYNKASSGKFHSHVVQVVQACKHIMSGVN*FLDVEIRQTTCTESY

Parental  PNLANCPFHDQPQLKKKALCSFQIYTVPWLGTTSLTKSSCQDA
          .NLA..PFHDQP...KKALCSF.IYTVPWLGTTS..KS.CQ.A
Retrocopy LNLATYPFHDQPHPRKKALCSFNIYTVPWLGTTSMMKSNCQNA

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_777 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010076	1 retrocopy	retro_amel_935,
Felis catus	ENSFCAG00000024003	1 retrocopy	retro_fcat_1975,
Loxodonta africana	ENSLAFG00000015020	1 retrocopy	retro_lafr_777 ,
Myotis lucifugus	ENSMLUG00000028312	2 retrocopies	retro_mluc_2081, retro_mluc_2613,
Mustela putorius furo	ENSMPUG00000001122	2 retrocopies	retro_mputfur_716, retro_mputfur_801,
Rattus norvegicus	ENSRNOG00000005195	1 retrocopy	retro_rnor_2853,