RetrogeneDB ID: retro_lafr_582

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_23:11735151..11736234(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKC1
• Ensembl ID: ENSLAFG00000000221
• Aliases: None
• Description: None

Sequence

>retro_lafr_582
ATTATAAAACCTGAATCCAAAGTTGCTCAGTTGGACACATCTCCGTGGTCCTTGTTGTTAAAGAATTTTGATTAGTTAAA
AGTAAGGATGAGACACTATACTCCTCTTCCTTCTGGTTCAAATCCTCTGAAGAGGGAGACTGCCGACTATATCAGGACAC
TTTTCGTTAACCTTGACAAGCCCTCTAACCCCTCTTCCCATGAGGTGGTAGCCTGGATCCGGTGGATACTTCATGTTGAG
AAGACAGGACACAGCGGTACTCTGGATCCCGAGGTGACTGGCTGTCTAATCGTGTGCACAGAACGAGCCACACTGGAGAA
ATCACAGCAGAGCACAGGAAAAGAGTATGTGGGAATTGTCCAGCTGCATGATGCCATGGAAGGGAGGACCCAGCTTTCTA
GAGCCCTAGAAACTCTGACAGGTGCCCTATTCTAGCTATCCCCCCTTATTGCTGCAGTCCAGAGGCAACTCCGAGTCCAG
ATCACCTGTGAGAGAAAAATGATAGAGTAGGATCCTGAGAGAAGATTAGGAATTTTTGGGGTGAGCTGTGAGGCTGACAC
CTACATTAGGACACTTTGTGTGCACCTTGGTTTGTTACTGGGAGTTGGAAGTCAGATGCAGGAACTTTGGAGGGTTTGTT
GTGAAGTTATGAGTGAAAAGGACCATATGGTGACAATGCGTGATGTGCTGGATGCTCAGTGGCTATACGATAATCACAAG
GATGAGAGTTACCTGCTGTGAGTTATTTACCCTCTGGAAAAGCTGCTGACATCTCACAAGCAACTGGTTATGAAAGACAG
TGCGGTGAATACAATATGCTGTAGAGCAAAGACTCTGGTTCCAGGTGTTCTTCAGTACAATGATGGCATTGAAGTCAATC
AGGAGATCATAGTCATCACCACCAAGGGGGAGGCCATCTGTATGGCTATTGCATTAATGACCACATCAATGATCTGGACC
TGTGACCATGGGATAGTAGCTAAGATCAAGAAAGTGATTGTGGAGAGAAATACATACCCACAGAAGTGGGGTTTAGGTCC
AAAGGCTAGTCAGAAGAGGATGATGCAGGGCTTTCTGGATCAG

Alignment

ORF - retro_lafr_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 70.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIKPESKVAQLDTSQWPLLLKNFDKLNVRTTHYTPLPSGSNPLKREIADYIRTGFINLDKPSNPSSHEVV
          .IKPESKVAQLDTS.W.LLLKNFD.L.VR..HYTPLPSGSNPLKRE.ADYIRT.F.NLDKPSNPSSHEVV
Retrocopy IIKPESKVAQLDTSPWSLLLKNFD*LKVRMRHYTPLPSGSNPLKRETADYIRTLFVNLDKPSNPSSHEVV

Parental  AWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHDAIEGGTQLSRALETL
          AWIR.IL.VEKTGHSGTLDP.VTGCLIVC.ERAT.L.KSQQS.GKEYVGIV.LHDA.EG.TQLSRALETL
Retrocopy AWIRWILHVEKTGHSGTLDPEVTGCLIVCTERAT-LEKSQQSTGKEYVGIVQLHDAMEGRTQLSRALETL

Parental  TGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQEL
          TGALF...PLIAAV.RQLRV....E.KMIE.DPERRLGIF.VSCEA.TYIRTLCVHLGLLLGVG.QMQEL
Retrocopy TGALF*LSPLIAAVQRQLRVQITCERKMIE*DPERRLGIFGVSCEADTYIRTLCVHLGLLLGVGSQMQEL

Parental  RRVRSGVMSEKDHMVTMHDVLDAQWLYDNHKDESYLRRVIYPLEKLLTSHKRLVMKDSAVNAICYGAKIL
          .RV...VMSEKDHMVTM.DVLDAQWLYDNHKDESYL..VIYPLEKLLTSHK.LVMKDSAVN.IC..AK.L
Retrocopy WRVCCEVMSEKDHMVTMRDVLDAQWLYDNHKDESYLL*VIYPLEKLLTSHKQLVMKDSAVNTICCRAKTL

Parental  LPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDTYPRKWGLGPKA
          .PGVL.Y.DGIEVNQEI.VITTKGEAICMAIALMTT..I.TCDHGIVAKIK.VI.ER.TYP.KWGLGPKA
Retrocopy VPGVLQYNDGIEVNQEIIVITTKGEAICMAIALMTTSMIWTCDHGIVAKIKKVIVERNTYPQKWGLGPKA

Parental  SQKRMMIKQGLLDK
          SQKRMM..QG.LD.
Retrocopy SQKRMM--QGFLDQ

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_582 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016095	1 retrocopy	retro_etel_1911,
Loxodonta africana	ENSLAFG00000000221	1 retrocopy	retro_lafr_582 ,
Rattus norvegicus	ENSRNOG00000048151	1 retrocopy	retro_rnor_2238,