RetrogeneDB ID: retro_lafr_1207

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_89:5791355..5791875(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INSIG1
• Ensembl ID: ENSLAFG00000028120
• Aliases: None
• Description: None

Sequence

>retro_lafr_1207
CACCTGGGAGCCTGCGCTGGAGGGCTGGCACCCAAAGTGGAAGACATGATCAGTCCTTCTGTGTCCAGCCCCTCTTTGCT
GGTGGACCACCGTGCCCCACACAGCAGCCCTTAGCCCAGGCGTCGCAGCACTAGTGTGAGTGGCCACCATTGCAGCAGCA
GTCGCCATGCTAATGGTTTGGCATCATCACTTGGTACAGAGGAGCCTTGTGCTATTTTCAGTTGGAGTTGTCCTAGTGTT
GGTGCTCAACCTGCCACAGATACAGAGGAATGTCATCCTTTTCCCTGAAGAAGTGTTTGCCACAATCTTCTCTTCTGCCT
GGTCTGTTCCTCCCTGTTGTGGGACAGCAACTGCTGTTGTAGGCTTGCTCTACCCCTGCATCGACAGTCATCTTGGAGAA
CCCCACAAGTTTAAGAGAGAGTGGGCCAGTGTAATGCGCTGTATCGCAGTTTTTGTTGGCATCAACTAAGAAAGTGCAAA
ATTGGATTTTGCCAATAATGTTCAGCTGCACTGGGTTTTG

Alignment

ORF - retro_lafr_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.29 %
• Parental protein coverage: 65.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HFWSCSCPASERHKKHLRAGAGGLAAKVDHGAPHSSPSPRRHSASVSGHHCSSSRHANS-WHHHLVQRSL
          H...C......................VDH.APHSSP.PRR.S.SVSGHHCSSSRHAN..WHHHLVQRSL
Retrocopy HLGACAGGLAPKVEDMISPSVSSPSLLVDHRAPHSSP*PRRRSTSVSGHHCSSSRHANG>WHHHLVQRSL

Parental  VLFSVGVVLALVLNLLQIQRNVTLFPDEVIATIFSSAWWVPPCCGTAAAVVGLLYPCIDSHLGEPHKFKR
          VLFSVGVVL.LVLNL.QIQRNV.LFP.EV.ATIFSSAW.VPPCCGTA.AVVGLLYPCIDSHLGEPHKFKR
Retrocopy VLFSVGVVLVLVLNLPQIQRNVILFPEEVFATIFSSAWSVPPCCGTATAVVGLLYPCIDSHLGEPHKFKR

Parental  EWASVMRCIAVFVGINHASAKLDFANNVQLSLTL
          EWASVMRCIAVFVGIN..SAKLDFANNVQL...L
Retrocopy EWASVMRCIAVFVGIN*ESAKLDFANNVQLHWVL

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_1207 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001982	1 retrocopy	retro_chof_1185,
Cavia porcellus	ENSCPOG00000014739	1 retrocopy	retro_cpor_1173,
Loxodonta africana	ENSLAFG00000028120	1 retrocopy	retro_lafr_1207 ,
Myotis lucifugus	ENSMLUG00000028113	1 retrocopy	retro_mluc_2270,
Rattus norvegicus	ENSRNOG00000006859	1 retrocopy	retro_rnor_159,