RetrogeneDB ID: retro_lafr_913

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_49:17370525..17371212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR4
• Ensembl ID: ENSLAFG00000032394
• Aliases: None
• Description: None

Sequence

>retro_lafr_913
ATGGCATGGTGGTGGTGGCTCCTGCTAGGGATGTGGACAGTCACGACTATGTGGTCTGGGGACAAGCTGCTCAATGTCTG
CATGAACACCAAACACCACGAGAAAGAGCCTAGCCCAGAAGACAAGCTCTAGGAGGAGTGCACCCCCTGGAAGGACAATG
CCTACTGCACAGCCAACACAGCTGGGAGGCCCACCTGGACATGTCCCTGCTCTACAACTTCAGCTTGGCTCATTGTGGGC
TGCTGACCCCCAGCTGTCAGAAGCACTTCATCCAGGCCTTCTGCTTCTACGAGTACTCTCCAAACCTGGGGCCTTGGATT
CGGCAGGTGGACCCGCGTGGGCAGGGAGGGGGCGTCGTGGGCGTGCGGCTGTGCCGGGAAGACTGTGAGCAGCGGTGGGC
TGACTGCCGCTTGTCCTACACGTGCAAATCCAACTGGCAGGGCAGCTGGGACTGGAGACGGGGAAGGTCCGCTGCCCTGC
AGGGGCTCACTGCCTCCGTTTCCCGATTACTTCCCCACCCCGGCTGACCTGTGAGAGATATCTGGAGCACCTCCTACACG
GCAAGCCCTGAGCGCCGCAACCAGTGGACGGTGTATACAGACGTGGTTTGAGCCCGCTCAGGGCAACCCCAATGTGGCTG
TGGCCCGCCTCTTCGCCAGCCCTGCCTGCTCCTGGTCTTGTCTCTGT

Alignment

ORF - retro_lafr_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.26 %
• Parental protein coverage: 94.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAWWWRLLLGMWTVTTTWSQDKLLNVCMNTKHHKTEPSPEDKLYEECTPWKDNACCTANT-SWEAHLDMS
          MAWWW.LLLGMWTVTT.WS.DKLLNVCMNTKHH..EPSPEDKL.EECTPWKDNA.CTANT.SWEAHLDMS
Retrocopy MAWWWWLLLGMWTVTTMWSGDKLLNVCMNTKHHEKEPSPEDKL*EECTPWKDNAYCTANT<SWEAHLDMS

Parental  LLYNFSLTHCGLLTPSCQKHFIQAFCFYECSPNLGPWIQQVDPRGQEEGIVGVPLCWEDCEQWWDDCRSS
          LLYNFSL.HCGLLTPSCQKHFIQAFCFYE.SPNLGPWI.QVDPRGQ..G.VGV.LC.EDCEQ.W.DCR.S
Retrocopy LLYNFSLAHCGLLTPSCQKHFIQAFCFYEYSPNLGPWIRQVDPRGQGGGVVGVRLCREDCEQRWADCRLS

Parental  YTCKSNWQGGWDWRR-GKVRCPAGAHCL-PFPDYFPTPADLCD-KIWSNSYKASPERR-SSGRCMQKWFE
          YTCKSNWQG.WDWRR.GKVRCPAGAHCL.PFPDYFPTPADL....IWS.SY.ASPERR..SGRC.Q.WFE
Retrocopy YTCKSNWQGSWDWRR<GKVRCPAGAHCL<PFPDYFPTPADL*E<DIWSTSYTASPERR>TSGRCIQTWFE

Parental  PAQGNPNVAVARLFANPARSWELSC
          PAQGNPNVAVARLFA.PA.SW...C
Retrocopy PAQGNPNVAVARLFASPACSWSCLC

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_913 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011928	2 retrocopies	retro_amel_1133, retro_amel_1192,
Equus caballus	ENSECAG00000007254	1 retrocopy	retro_ecab_415,
Loxodonta africana	ENSLAFG00000032394	1 retrocopy	retro_lafr_913 ,
Sus scrofa	ENSSSCG00000014952	1 retrocopy	retro_sscr_282,