RetrogeneDB ID: retro_lafr_1141

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_76:4501241..4501974(-)
• Located in intron of: ENSLAFG00000018339

Retrocopy information

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

Parental gene information

• Parental gene symbol: IP6K2
• Ensembl ID: ENSLAFG00000022060
• Aliases: None
• Description: None

Sequence

>retro_lafr_1141
CAAGTCTTCCATTACAGTGTAGAAAAAAGGGGAAACATGAGTTCCCAGCTTCAACACTATAACCCTTGGAGCATCCAGTG
TCACCAGCAAGTTACAGCGAATGAATGAGAACGTGAAGCACCGTAACCAGTACAAATTTATTTTACTGGAGAACCTGACC
CCTCACTATGAGACGCCCTGTGTCCTGAGCCTCAGGATGGGTACACACCAGAATGGCGACAATGCTTCAGAGGAGAAGGC
AGCCAACCAGATCTGCAAGTGGCAGCAGAGCATATCTGTGGTCATGGTGGTACACACGTGTGGCATGCAGGTGTACTAGA
CAGGCAGCAGACAGCTCGTGTTTATGAGCAAGTACCATGGGCGAAGGCTATCAGTGCAGGGCTTCAAGGAGGCAATTTTC
CAGTTCTTCTACAACGGGCAATACCTGCACCAACATCTCCTGGGCCCTTTGCTCAAGAAGCTGGCTGAGCTTAAGGCAGT
GCTAGAGTGACAGGAATCCTATAGCTTCTATTCAAGCTCCCTGCTGGTCATCTACAATGGTAAAGAGCGGTCGGAGGTGG
CCCTGGACTCAGATACTGAAGGACTTGGAGGACCTGTCAGAGGAGTCAGCCCAAAAGTCTGCCGGTGCTTACGCCTACAA
GCCCATTGGCACCAACTCAGTGGACGTGCATATGTTTGACTTTGCACACACCATCTGCAGGCTATATGGCAAGGACAGCT
GGTGCATAAGGGC

Alignment

ORF - retro_lafr_1141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 57.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVLYYSVEKKGNVSSQLKHSNPWSMKCHQQQ-LQRMKENVKHRNQYKFILLENLTSRYEVPCVLDLKMGT
          .V..YSVEK.GN.SSQL.H.NPWS..CH.QQ.LQRM.ENVKHRNQYKFILLENLT..YE.PCVL.L.MGT
Retrocopy QVFHYSVEKRGNMSSQLQHYNPWSIQCH-QQ>LQRMNENVKHRNQYKFILLENLTPHYETPCVLSLRMGT

Parental  RQHGDDASEEKAANQIRKCQQSTSAVIGVRVCGMQVYQAGSGQLMFMNKYHGRKLSVQGFKEALFQFFHN
          .Q.GD.ASEEKAANQI.K.QQS.S.V..V..CGMQVY..GS.QL.FM.KYHGR.LSVQGFKEA.FQFF.N
Retrocopy HQNGDNASEEKAANQICKWQQSISVVMVVHTCGMQVY*TGSRQLVFMSKYHGRRLSVQGFKEAIFQFFYN

Parental  GRYLRRELLGPVLKKLAELKAVLERQESYRFYSSSLLVIYDGKERPEVALDSDAE-DLEDLSEESADESA
          G.YL...LLGP.LKKLAELKAVLE.QESY.FYSSSLLVIY.GKER.EVALDSD.E.DLEDLSEESA..SA
Retrocopy GQYLHQHLLGPLLKKLAELKAVLE*QESYSFYSSSLLVIYNGKERSEVALDSDTE>DLEDLSEESAQKSA

Parental  GAYAYKPIGTSSVDVRMIDFAHTTCRLYGEDS-VVHEG
          GAYAYKPIGT.SVDV.M.DFAHT.CRLYG.DS..VH.G
Retrocopy GAYAYKPIGTNSVDVHMFDFAHTICRLYGKDS<LVHKG

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_1141 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000022060	1 retrocopy	retro_lafr_1141 ,