RetrogeneDB ID: retro_lafr_833

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:15900208..15900828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT19
• Ensembl ID: ENSLAFG00000032048
• Aliases: None
• Description: None

Sequence

>retro_lafr_833
GGGCCGGAGCCAGGCTGCGCTCTCCCGCCGCCGCCTTACCTGGCCGCTGGGCGCATTCGCGTCCGCAGCGACCCACGCCA
CTTCCCACGCCTGTGCGCGCGCCTGGGCTGCTCGCCGGACATCTGGGCGCTGCACGACTGGAGCGCCTGGCTGCCACCGC
TCGTGCGCCCCGGCGGCCCTCGCTTGGACAGGGCCTTCCTTCCGTGCTGCCTGAGCTAACCGCTGGCCGCGGGTCCGGAC
GTGGCCAGGGTGGTGGGCTGCTAGTGGTCATCTCCGTCAGAAGCAACTGAAAGGTTCCTATCAAAAGCAATTTGGTTGGC
ACCCTTACAGTTCTACCAAATAAGAAGACTAGAAAATTTGGCCTCTCTTTCAGACTTGCACAAATTGTGTTTGCATCGCG
CCTTAGAAGGGAGGGAAGGATGGCTGCCGAGCACATTATTAACTGCTGATGGGGCACTCCAGCTTTTACCGGGAGCTGCA
GTGTACTGGGAAGATTCAGACACTTTAGAAAATAATGTATCCACTGAGAAAAAATTGAAGACATCATGAAGGAGGGCAAG
AAATTTCACTGAGTAGTGATGTGTGATCGCCATCTTTGTAATATCCGCGTGACTGTTCAA

Alignment

ORF - retro_lafr_833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 60.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPEPCCALAPLPDLDAWRARVRSDARHFLHLCAHLDCTPDIWALHDWSAWLTPFWKARA--VDTAFFLCC
          GPEP.CAL.P.P.L.A.R.RVRSD.RHF..LCA.L.C.PDIWALHDWSAWL.P.........D.AF..CC
Retrocopy GPEPGCALPPPPYLAAGRIRVRSDPRHFPRLCARLGCSPDIWALHDWSAWLPPLVRPGGPRLDRAFLPCC

Parental  LREPPAACPDMAEVVDCQWLSPSEATESFLSEEIWLAPPQFYEIRRLENFASLSDLHKFCLDHASEGRER
          L..P.AA.PD.A.VV.C.W.SPSEATE.FLS..IWLAP.QFY.IRRLEN.ASLSDLHK.CL..A.EGRE.
Retrocopy LS*PLAAGPDVARVVGC*WSSPSEATERFLSKAIWLAPLQFYQIRRLENLASLSDLHKLCLHRALEGREG

Parental  WLPIMLLTTDGTLHLLPGDELYLEDSDHLENNLSTEK-KIEDIMKEGKKFHRVVIHDRHLYSVHVTIQ
          WLP..LLT.DG.L.LLPG...Y.EDSD.LENN.STEK.KIEDIMKEGKKFH.VV..DRHL....VT.Q
Retrocopy WLPSTLLTADGALQLLPGAAVYWEDSDTLENNVSTEK<KIEDIMKEGKKFH*VVMCDRHLCNIRVTVQ

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_833 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000032048	1 retrocopy	retro_lafr_833 ,
Nomascus leucogenys	ENSNLEG00000007633	1 retrocopy	retro_nleu_507,