RetrogeneDB ID: retro_lafr_1256

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_99:974992..975771(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000010293
• Aliases: None
• Description: None

Sequence

>retro_lafr_1256
AAGATAGCATATCCCCAGCCAGACCTGCATACACCCTCTAGGAAAGATAACCTCGTTTTGACCCCTTGGCTGGCTCCCGT
TGTCTGGAAGGGGACCTTCAATATTGACATTCTGAACGAGCAGTTCCGACTCCAGAACGCCACCATTGGGTTAACTGTGT
TTGCCGTAAAAAAAATACGTGATCTTTCTGAAGCTGTTCCTGCAGACGGCAGAGAAGTACTTCATGATGGGACACAGGGT
CAACTAGTACATCTTCACTGATCTGCCAGACAGTGTGCTCCGAGTTCCCCTCCAAGAAGGAAGACAGGTGGTCATCCTCA
AGGTGCAGAGCTATACCTGCTGGCAAGACATCTCCATGTACCGTATGGAAATGATTAGCAATTTCTCCAAGCAGCGCTTC
CTTGGTGAGGTGGACTACCTGATGCGTGCTGATGTGGACATGAAGTCCAGTGATCACGTGGGGGTGGAGGTCCTCTCCTC
TTTGTTCAGCACCCTTCATCCTGGCTTCGTTGGGATCAGTAGGCTTGGCTTCACCTATGAACACTGGCCTCAATCACAAG
CCTATATTTCCGAGGATGAAGGAGACTTTTACTATATAGTGGCCCTTTTTGGGGGGTCAGTGCTGGAAGTTTACTGGCTC
ACCAAGGCCTGTCACGAGGTGATGATGGTCGACCAAGCCAATGACATTGAAGCTATATGGCATGAGGAGAGCCACTTGAA
CAAGTACCTGCTTTACTACAAACCTACCAGAGGTCCTCTCCCCAGAGTACATGTGGGAT

Alignment

ORF - retro_lafr_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.95 %
• Parental protein coverage: 73.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RMMYPQPKVLTLCRSDVLVLTPWLAPIVWEGTFNIDILNAQFQLQNATIGLTVFAIKK-YVVFLKLFLET
          ...YPQP...T..R.D.LVLTPWLAP.VW.GTFNIDILN.QF.LQNATIGLTVFA.KK.YV.FLKLFL.T
Retrocopy KIAYPQPDLHTPSRKDNLVLTPWLAPVVWKGTFNIDILNEQFRLQNATIGLTVFAVKK>YVIFLKLFLQT

Parental  AEKYFMVGHKVNYYVFTDRPADVPPVPLQEGRQVVVLQVRNYTRWQDVSMHRMEMISSFSRQRFLREVDY
          AEKYFM.GH.VN.Y.FTD.P..V..VPLQEGRQVV.L.V..YT.WQD.SM.RMEMIS.FS.QRFL.EVDY
Retrocopy AEKYFMMGHRVN*YIFTDLPDSVLRVPLQEGRQVVILKVQSYTCWQDISMYRMEMISNFSKQRFLGEVDY

Parental  LVCADVDMKFSDHVGVEILSSLFGTLHPGFYAADRQAFTYERRPLSQAYIPRDEGDFYYAGGFFGGSVLE
          L..ADVDMK.SDHVGVE.LSSLF.TLHPGF....R..FTYE..P.SQAYI..DEGDFYY....FGGSVLE
Retrocopy LMRADVDMKSSDHVGVEVLSSLFSTLHPGFVGISRLGFTYEHWPQSQAYISEDEGDFYYIVALFGGSVLE

Parental  VHRLTKACHQAMMVDQANHIEAVWHDESHLNKYLLYHKPTK-VLSPEYVWD
          V..LTKACH..MMVDQAN.IEA.WH.ESHLNKYLLY.KPT..VLSPEY.WD
Retrocopy VYWLTKACHEVMMVDQANDIEAIWHEESHLNKYLLYYKPTR>VLSPEYMWD

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_1256 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001005	1 retrocopy	retro_amel_1927,
Bos taurus	ENSBTAG00000012525	1 retrocopy	retro_btau_699,
Loxodonta africana	ENSLAFG00000010293	1 retrocopy	retro_lafr_1256 ,
Mustela putorius furo	ENSMPUG00000012419	1 retrocopy	retro_mputfur_1076,