RetrogeneDB ID: retro_lafr_849

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:96789526..96790119(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA1
• Ensembl ID: ENSLAFG00000005238
• Aliases: None
• Description: None

Sequence

>retro_lafr_849
TTGGAAAATGAGTATCAAGAACAAACCAGCAGTTCTCTCAAGGAACTCTGTGAATCTCTTGAAGAAGATTATAAAGATGT
GCAGCATTTTGAAGAAAACATTCCTCCCCATTTGCCTCAAGTAGCAGTAACCAATAGCTTTGCTAACGGATCAGATCTTA
GCTCTGAACAACCAGTCAAAGTTGTGGAACCTGTACCCATAAATGAGCCCCCAAAAGGACAAAGAAATATTAAGGAAATG
CCATTTATAACTTCTGATGAGTTCAACGGTATTCCTGCATACATGAAATCCCGGTTAACCTATTCTCAAATTGATGATAT
TGTTGAAGAAATCAACAAGGCAGTAGCTAGTAAATATAAAATCTTACATCAACCAAAAAGTCTATGCATTCTGTGGCCAG
AAACCTCTATCACAGATTTACTGAAGAAGAAACAAATGATACCAAAACTCATTGTTTTATAGTGGAAGCTGACATAAAGG
AGTTCACGGCTTTGAAAGCTGACAAGAGGTTTCATGTGATAGTGAATATTTTACGACAGTGCAGGAGGCTCTCAGAGGTC
CCAGGGGGAAGACTGGCCAGTTATGTTATAACC

Alignment

ORF - retro_lafr_849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 77.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEIEYQEQTSNSLKELCESLEEDYKDVQHLKENIPPHLPQVTVTKSIAKGADLTSEEPAKVVEPAPGNKP
          LE.EYQEQTS.SLKELCESLEEDYKDVQH..ENIPPHLPQV.VT.S.A.G.DL.SE.P.KVVEP.P.N.P
Retrocopy LENEYQEQTSSSLKELCESLEEDYKDVQHFEENIPPHLPQVAVTNSFANGSDLSSEQPVKVVEPVPINEP

Parental  PKGQRNIKEMLFITSDEFNGIPAYMKSRLTYCQINDVIKEINKAVASKYKILHQP-KKSMSSVARNLYHR
          PKGQRNIKEM.FITSDEFNGIPAYMKSRLTY.QI.D...EINKAVASKYKILHQP.KKSM.SVARNLYHR
Retrocopy PKGQRNIKEMPFITSDEFNGIPAYMKSRLTYSQIDDIVEEINKAVASKYKILHQP<KKSMHSVARNLYHR

Parental  FIDEETKDTKGHCFIVEADIKEFTALKVDKRFHVILNILRHCRRLSEVRGGGLTRYVIT
          F..EET.DTK.HCFIVEADIKEFTALK.DKRFHVI.NILR.CRRLSEV.GG.L..YVIT
Retrocopy FTEEETNDTKTHCFIVEADIKEFTALKADKRFHVIVNILRQCRRLSEVPGGRLASYVIT

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_849 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008555	2 retrocopies	retro_cjac_1103, retro_cjac_875,
Dasypus novemcinctus	ENSDNOG00000000190	1 retrocopy	retro_dnov_1081,
Loxodonta africana	ENSLAFG00000005238	1 retrocopy	retro_lafr_849 ,
Myotis lucifugus	ENSMLUG00000013388	1 retrocopy	retro_mluc_2127,
Sus scrofa	ENSSSCG00000004518	1 retrocopy	retro_sscr_360,
Tursiops truncatus	ENSTTRG00000015539	1 retrocopy	retro_ttru_1083,