RetrogeneDB ID: retro_lafr_23

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:91111064..91111772(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000032132
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSLAFG00000000171
• Aliases: None
• Description: None

Sequence

>retro_lafr_23
GTGTCAGTGGAGCCGCACCGGCACGAGGGCGTCTTCATCTACCGCGGAGCGGAGGACGCGCTGGTCACGCTGAACCTGGT
GCCGGGCCAGTCGGTGTACGGCGAGCGGCGCGTCACGGTGACCGAGGGCGGCGTGAAGCTGGAGTACCGCACGTGGAACC
CCTTCCGCTCCAAGCTGGCCGCGGCCATCCTGGGCGGGGTCGACCAGATCCACATTAAGCCCAAGTCCAAAGTGCTGTAC
CTGGGGGCCGCCTCGGGGACCACTGTCTCCCATGTTTCCGACATCATCGGCCCGGATGGCCTGGTCTACGCGGTCGAGTT
TTCGCATCGTGCCGGCCGTGATCTGGTCAACGTGGCCAAGAAGCGAACCAACATCATCCCGGTCCTCGAGGATGCCCGGC
ATCCGCTCAAGTACCGCATGCTCATCGGGATGGTGGACGTGATCTTCGCCGATGTGGCCCAGCCGGATCAGTCTCGCATC
CTGGCCCTGAACGCCCACACCTACTTGCGCAATGGCGGCCACTTCCTCATTTCCATCAAGGCCAACTGCATCGACTCCAC
GGCATCTGCCGAGGCAGTGTTTGCTTCTGAGGTGAGGAAGTTGCAGCAGGAGAATTTGAAGCCGCAAGAACAGCTGACCC
TGGAGCCCTATGAGAGGGACCACGCTGTGGTCGTTGGGGTCTACCGACCTCCTCCCAAGAGTAGCAGC

Alignment

ORF - retro_lafr_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 73.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQI
          V.VEPHRHEGVFI.RG.EDALVT.NLVPG.SVYGE.RV...EG..K.EYR.WNPFRSKLAAAILGGVDQI
Retrocopy VSVEPHRHEGVFIYRGAEDALVTLNLVPGQSVYGERRVTVTEGGVKLEYRTWNPFRSKLAAAILGGVDQI

Parental  HIKPGAKVLYLGAASGTTVSHVSDIVGQDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRM
          HIKP..KVLYLGAASGTTVSHVSDI.G.DGLVYAVEFSHR.GRDL.N.AKKRTNIIPV.EDARHP.KYRM
Retrocopy HIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLEDARHPLKYRM

Parental  LIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQE
          LI.MVDVIFADVAQPDQ.RI.ALNAHT.LRNGGHF.ISIKANCIDSTASAEAVFASEV.K.QQEN.KPQE
Retrocopy LIGMVDVIFADVAQPDQSRILALNAHTYLRNGGHFLISIKANCIDSTASAEAVFASEVRKLQQENLKPQE

Parental  QLTLEPYERDHAVVVGVYRPPPK
          QLTLEPYERDHAVVVGVYRPPPK
Retrocopy QLTLEPYERDHAVVVGVYRPPPK

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_23 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23 ,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30,