RetrogeneDB ID: retro_lafr_1127

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_72:4920526..4921421(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC109B
• Ensembl ID: ENSLAFG00000002726
• Aliases: None
• Description: None

Sequence

>retro_lafr_1127
AAACTACATGGAAATCTGAAATATTATCTATCACGCCTTTGTAGTACAGTGGTGCCACCTGATGAAGTAACAGTTAATTA
TAGATATGACCTTCCTTTGATAACACTTCCTTTGCCATCCAGCAGAGAGCGGTGTCAATTTGAAGTCAAACCACTGTTAT
CAACTGTTGGTTCATTCCTTCAGGAAATATAAAATGAAGATACAGGTGTCAAAACCGCAGCCACCTTCACAGAAGATGGC
AACAAGATTCCAGTTATATCCTTGATGGGAATTTTGCTAATGAATGATTTTAAACTTGTCGTCAATAAAATAACCTATGA
TGTGCAGTGCCTGAAGCAAGAAAAGCTGAGCAGAGAGCATGCTATTGAGATGGAAACCATGATGTCTTTGGTTCACAGAC
TGTGTACAGCCTTACATTTTGATGAATTTCGGAAAAAGAAAGAGAACCATTTACTGAAGAAAGCCGACCACCTGAAGAAA
CAGCTGCAGCCCCTTAAGAGCTGAAAGCTAGCGTCGAAGGTCGCTCTGAAGCCGGAATCAGCAGACTCCCATGGACTGGA
TTGGCACTGCTGTCCATTCAGGGCACGGCACTGGCTTGGTTCGCTTGGTGGGTTTACTCCTGGGGCATCATGGAACCAGT
TACATGCTTCATTACATTTGCAAATTCCATGGTCTCTTTTGCATACTTTCTAGTGACTAGACAGGATTATGCTTACTCAG
CTGTTAGTGCTAGGCAGCTTCTTCACTTCTTCTATAAGAAATCAAAGGAAGAGCATTCTAATATGGAGCAGTACAGCCTG
TTAAAGACGACCTTGGTGAGGCTTAAGAAACCCTGAAATGATTTTGCCATATTCTCTATTTTCGATTGCCAATGGAGGAA
CTCAATGGCAGGAAT

Alignment

ORF - retro_lafr_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVCGNLKYYLSPLYSTVVPSDAEITVNYRYGLPLITLPLPSRRERCQFVVKPMLSTVGSFLQEIQNEDKG
          K..GNLKYYLS.L.STVVP.D.E.TVNYRY.LPLITLPLPS.RERCQF.VKP.LSTVGSFLQEI.NED.G
Retrocopy KLHGNLKYYLSRLCSTVVPPD-EVTVNYRYDLPLITLPLPSSRERCQFEVKPLLSTVGSFLQEI*NEDTG

Parental  VKTAAIFTADGSKIPASTLMGILLMSDFKLVINKITYDVQCPKQEKLSSEHATEMETMMSLVHRLFTAIH
          VKTAA.FT.DG.KIP...LMGILLM.DFKLV.NKITYDVQC.KQEKLS.EHA.EMETMMSLVHRL.TA.H
Retrocopy VKTAATFTEDGNKIPVISLMGILLMNDFKLVVNKITYDVQCLKQEKLSREHAIEMETMMSLVHRLCTALH

Parental  FDEYRKKKENHLLEKIDHLKKQLQPLE-QLKARVEGRSEARISRLLWTGLALLSIQGGALAWFTWWVYSW
          FDE.RKKKENHLL.K.DHLKKQLQPL...LKA.VEGRSEA.ISRL.WTGLALLSIQG.ALAWF.WWVYSW
Retrocopy FDEFRKKKENHLLKKADHLKKQLQPLK<ELKASVEGRSEAGISRLPWTGLALLSIQGTALAWFAWWVYSW

Parental  DIMEPVTYFITFANSMVFFAYFLVTRQDYTYSAVSGRQFLHFFYKKSKQEHFDVEQYNRL-KDDLDEAKE
          .IMEPVT.FITFANSMV.FAYFLVTRQDY.YSAVS.RQ.LHFFYKKSK.EH...EQY..L.KDDL.EA.E
Retrocopy GIMEPVTCFITFANSMVSFAYFLVTRQDYAYSAVSARQLLHFFYKKSKEEHSNMEQYSLL<KDDLGEA*E

Parental  ALKRLRHILYFRLPVEELNDKN
          .LK...HILYFRLP.EELN..N
Retrocopy TLK*FCHILYFRLPMEELNGRN

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_1127 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
Echinops telfairi	ENSETEG00000013586	1 retrocopy	retro_etel_443,
Loxodonta africana	ENSLAFG00000002726	1 retrocopy	retro_lafr_1127 ,
Ochotona princeps	ENSOPRG00000017044	1 retrocopy	retro_opri_646,
Vicugna pacos	ENSVPAG00000009837	1 retrocopy	retro_vpac_642,