RetrogeneDB ID: retro_lafr_333

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_122:440671..441906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RYK
• Ensembl ID: ENSLAFG00000016402
• Aliases: None
• Description: None

Sequence

>retro_lafr_333
GAATTTGAAGAAGTAAAAACTTCAGCCTTGGACAAAAGCACTAGCAGAACTACTTATGATCCTGTACCTGCGGCTCCAGC
TACTTCTACACATGTGTTTTATATCAGTGTGGGGGGTTGCTGTGCGGTAATGTTTCTTGTAGCAATAATATCAGCTGTTC
TGCACCTTCATTGTGTCAAAAGGATTGAACTGGATGACAGCATCAGTGCCAGCAGTAGTTCCCAAGGGCTGTCTCAGCCA
TCTACCCAGAGAACTCAGTATCTGAGAGCCCACACGCCCAACAATGCAACTCCCATCACCAACTCCTCAGGTTATCCTAC
CTTGTGGATAGAGAAGAAGGACCTGAGAAGTGTCACTCTTTTGGAGGCCAAAGCCAAAATGAAGGATATAGCAATATCCA
GGGAAAGGATAACCCCAAAACGTGTACTCTGACAAGGCATTTTTGGACTTATTTTCCATGAGATTTTAATGGATGAAAAA
GATCCAAATAAAGAAAAACAAACATTTATGAAAACACTTAAAGATCAAGCTCCTGAAATTCAGGTGACAGTGATGCTTAC
TGAAAGTTGTAAGCTATGAGGCCTTCATCACAGAAATCTTCCTGTTACCCATGTGTGTATAGAAGAAGGAGAAAAGCCCA
TGGTGATATCGCCTCACATGAATTGGGAGAATCCTAAATTGTTCTTACAGTTGTGCAAATTAGAGAGGCCAATAATTCTC
AGGCAATTTCTCAGCAAGACCTGGTAACCTGGCCATTCAGATTGCCTGTGGAATGAGCTATCTGGCCAGAAGGGAAGTCA
TCTACGAAGACCTGGCTGCTAAGAACTGTGTCACTAATGATACATTTCAAGTTAAGGTCATAGACAATGCCCTCTCCAGA
GACTTGTTCCTCATGGACTATCATTGACTGGGGGACAATGAAAACTGGCCAGTTTGGCAACTGGCTCTTGAAAGTCTAGT
TGATAATCAGTTCTCCAGCGCTAGCGATGTGTGGGCCTTCGGAGTGGCGCTGTGGGAGCTCATGACACTGAGCCAGATGC
CATATGTAGACATCGACCCCTTTGAAATGGCTGCATACCCGAAAGACGGCTACCAAATACCTCACTCAATCAACTGTCTT
CAACTATTTGCCGTGACGGCCTGTTGTTCGGTCTTAGATGCAGAGAGAGGTCCCAGTTTCAGCAGCTGGTACAACATCTC
ACAGAGTTCCATGCAGCTCTGGGGGCCTCTGTCTG

Alignment

ORF - retro_lafr_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.95 %
• Parental protein coverage: 77.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KFEEVKTSALDKNTSRTIYDPVHATPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDDSISA
          .FEEVKTSALDK.TSRT.YDPV.A.P.TST.VFYISVG.CCAV.FLVAII.AVLHLH..KRIELDDSISA
Retrocopy EFEEVKTSALDKSTSRTTYDPVPAAPATSTHVFYISVGGCCAVMFLVAIISAVLHLHCVKRIELDDSISA

Parental  SSSSQGLSQPSTQTTQYLRADTPNNATPITSSSGYPTLRIEKNDLRSVTLLEAKAKVKDIAISRERITLK
          SSSSQGLSQPSTQ.TQYLRA.TPNNATPIT.SSGYPTL.IEK.DLRSVTLLEAKAK.KDIAISRERIT.K
Retrocopy SSSSQGLSQPSTQRTQYLRAHTPNNATPITNSSGYPTLWIEKKDLRSVTLLEAKAKMKDIAISRERITPK

Parental  DVLQEGTFGRIFHGILLDEKDPNKEKQTFVKTVKDQASEIQVTMMLTESCKLRGLHHRNLLPITHVCIEE
          .VL..G.FG.IFH.IL.DEKDPNKEKQTF.KT.KDQA.EIQVT.MLTESCKL.GLHHRN.LP.THVCIEE
Retrocopy RVL*QGIFGLIFHEILMDEKDPNKEKQTFMKTLKDQAPEIQVTVMLTESCKL*GLHHRN-LPVTHVCIEE

Parental  GEKPMVILPYMNWGNLKLFLRQCKLV-EANNPQAISQQDLV-HMAIQIACGMSYLARREVIHKDLAARNC
          GEKPMVI.P.MNW.N.KLFL..CKL..EANN.QAISQQDLV...AIQIACGMSYLARREVI..DLAA.NC
Retrocopy GEKPMVISPHMNWENPKLFLQLCKLE<EANNSQAISQQDLV<NLAIQIACGMSYLARREVIYEDLAAKNC

Parental  VIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELMTLGQT
          V..DT.QVK..DNALSRDLF.MDYH.LGDNEN.PV...ALESLV.N.FSSASDVWAFGV.LWELMTL.Q.
Retrocopy VTNDTFQVKVIDNALSRDLFLMDYH*LGDNENWPVWQLALESLVDNQFSSASDVWAFGVALWELMTLSQM

Parental  PYVDIDPFEMAAYLKDGYRIAQPINCPDELFAVMACCWALDPE-ERPKFQQLVQCLTE-SMQPW-SLCL
          PYVDIDPFEMAAY.KDGY.I...INC...LFAV.ACC..LD.E.ER..FQQLVQ.LTE.SMQ.W..LCL
Retrocopy PYVDIDPFEMAAYPKDGYQIPHSINCL-QLFAVTACCSVLDAE<ERSQFQQLVQHLTE>SMQLW>GLCL

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_333 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016999	2 retrocopies	retro_btau_790, retro_btau_793,
Loxodonta africana	ENSLAFG00000016402	1 retrocopy	retro_lafr_333 ,
Tursiops truncatus	ENSTTRG00000003760	1 retrocopy	retro_ttru_44,