RetrogeneDB ID: retro_lafr_171

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:114838103..114839109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000003257
• Aliases: None
• Description: None

Sequence

>retro_lafr_171
ATGGTTTTAGATATCAGAAAACCCTCTCAATGTGAACCATCCGGGAATGATCCTGGGTCAGAAACTCAAGAGCTTGAACA
CATCCAAAGACTTGGTGCCCAGAAGGGAGATGGTGTCTCTGGGCTCCAGAACACTCCACTCAGCATATTTTAGTACAGCA
ATAACTCATATGTAATACAGGAACTGAAGAGACTCTAGAAGTTATTTCACTTATGGCTGCAGCCAGAGAAACACAGCAAG
GAGGAAATGATTTCCCAATTGGCCCTGAACAGTTTATGATGAATGAGCACTGCAGAAATAGGTCCCCTTTGAAAGAGAAA
TTGGATTCAATTGGCAGGAGCCTGAAGAACTTCATGGAAAATCTGACTGCTGATTGCATAGAGCCACCTGGCTTTGTTCA
TGTTCTCATGCAGGGACAGGAAACCCTCTTTTCCAAGAATATGCTCTTAAGAGACATCATTGTTCACCTTACAGAACAGT
TGTCTGCAGGGACCCCAACAGGAGAGAACATGGGGACTCCCTTCCTGACTCAAGATCCTCCCACACAAACAGACGAGGAG
GTGAAGATAAAGAAGACAGCAGCAACCTTTCTTTGAAAACCATGCAAGTAAACGGCAGTACTACTAGCCGAGACAATCAA
GTGTTTTCCCCACGGGTTATTCAGGAAGAGAATTATCTCAAACCTGAAGAAGGAGGTCTTGCTGGGACAATCCAGAAAGC
TCCAGAAAAGCAGGGCTAGGTACATCCAAGTCCCAGGAAAGGGCTCTGGGAGGACTCTATCATCAAGATGTTCCTGTGGA
GGTGGAGCCAAGATTTATCTCCAGGCCAGACCCAGCCACCCCGATCCTGTCCCTGCCCACAGAGCAATGAGGGTAAATCC
ACAGGTGGAGGACACCAAGAAAAATTTCATGAAACTCCAAAACCATACAGATGTGGGGATTGTCCCAAGAACTTTAGGTA
TTTCTCTTAGTTAGAAGTCCACCAGAGAAGACACAGGAACAAGAGG

Alignment

ORF - retro_lafr_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MALDLRTPFRCEPSRNAPRLENLEFEPTQGPDVQKPERISGLQGTPLNIYQYSNNSYAKQELQRLQKLFD
          M.LD.R.P..CEPS.N.P..E..E.E..Q....QK....SGLQ.TPL.I..YSNNSY..QEL.RL.KLF.
Retrocopy MVLDIRKPSQCEPSGNDPGSETQELEHIQRLGAQKGDGVSGLQNTPLSIF*YSNNSYVIQELKRL*KLFH

Parental  LWLQPEKYSKEEMISQLVL-EQFMMNEQCRNRSNLKEKWDSSGRNLQKFPEDLTDDFMEPPAYVHICMQG
          LWLQPEK.SKEEMISQL.L.EQFMMNE.CRNRS.LKEK.DS.GR.L..F.E.LT.D..EPP..VH..MQG
Retrocopy LWLQPEKHSKEEMISQLAL<EQFMMNEHCRNRSPLKEKLDSIGRSLKNFMENLTADCIEPPGFVHVLMQG

Parental  QEALCSENMPLKDIIVHLTKQLSAGTPIGENMETPFQTPQDPPMQTG-KGGEDKEDSSKLSLKTTQVNNS
          QE.L.S.NM.L.DIIVHLT.QLSAGTP.GENM.TPF.T.QDPP.QT...GGEDKEDSS.LSLKT.QVN.S
Retrocopy QETLFSKNMLLRDIIVHLTEQLSAGTPTGENMGTPFLT-QDPPTQTD<RGGEDKEDSSNLSLKTMQVNGS

Parental  ITSGGNQVLSLQIIQEENCPKPEEA-HACWDNPESSRRAGLGTSGSQEKALGGPFHQDVPVELEQGFISR
          .TS..NQV.S...IQEEN..KPEE....CWDNPESSR.AGLGTS.SQE.ALGG..HQDVPVE.E..FISR
Retrocopy TTSRDNQVFSPRVIQEENYLKPEEG<RSCWDNPESSRKAGLGTSKSQERALGGLYHQDVPVEVEPRFISR

Parental  PDPTT-PESAPALQ-SKEEKSPGRRYQERFHETPKPYRCEDCPKIFKYFSQLEAHQRIHLQEK
          PDP.T.P...PA...S.E.KS.G...QE.FHETPKPYRC.DCPK.F.YFS.LE.HQR.H....
Retrocopy PDPAT<PDPVPAHR<SNEGKSTGGGHQEKFHETPKPYRCGDCPKNFRYFS*LEVHQRRHRNKR

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_171 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171 ,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,