RetrogeneDB ID: retro_lafr_562

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_21:36045810..36046648(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030753
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TIA1
• Ensembl ID: ENSLAFG00000003463
• Aliases: None
• Description: None

Sequence

>retro_lafr_562
ATGGAAGACGAGATGCCCAAGACTCCAAATGTCGGTAATCTTTCCAGAAACGTGACAGAAGCTCTAATTCTCCAGCTCTT
CAGCCAAATTGGACCTTGTAAAAATTGCGAAATGATTATAGATGCGGCTGGAAATGATCCATATTTTTTTAGAGAGTTTT
ATGAACATCATCACGCAGCTGCAGCACTACCTGCTATGAATGGGTGGAAGATAATGAGTAAGGAAGTCAAAGTCAAACAA
CTTCCAGCAGTCAAAAGAAAGATACAAGCAGTAGTACGGTTGTCAGCACACAGTATTCACCAGCTCATTTCCATGTCTTT
GTTGGTTATTTCAGTCCAGAAATTTACAACTGAAGATATAAAAGCTGCTTTTGTACCATTTGGAAGAATATCAAATGCCC
ATGTGTTTAAAGACATGGCAACAGGAAAGTCTAGGGGTTATGGCTTTGTCTCATTTTTCAACAAATGGGAAGGCGAAAAC
ACCATTGAACAGATGGGTGACCAGTGGCTCGGTGGATGATAAATGAGAACTAACTGGGCAATGCAAAAGCCTCCAGGCTC
CAAAGAGTACACATGAGTCAAACACTGAACAGCTATCATATGATGAGGTTGTAAATTAGTCTAGTCCAAGCAGCTGTACT
GTATACTGTAGAGGTGTTACTTCTGGACTAAGAGAACAACTAATGCATCAGACTTTTTTACCATTTGGACAAATAATGGA
AATTTGTATCTTTCCAGACAAAAGATGTTCATTTGTTCGGTTCAATTCTCATGAAAGTGCAGCATATGCAATTATTTCTG
TTATTGGTACTACCATTGAAGATCATGTTATGAAATGT

Alignment

ORF - retro_lafr_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 72.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEDEMPKTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFYEHRHAAAALAAMNGRK
          MEDEMPKT..VGNLSR.VTEALILQLFSQIGPCKNC.MI.D.AGNDPY.F.EFYEH.HAAAAL.AMNG.K
Retrocopy MEDEMPKTPNVGNLSRNVTEALILQLFSQIGPCKNCEMIIDAAGNDPYFFREFYEHHHAAAALPAMNGWK

Parental  IMGKEVKVNWATTPSSQKK-DTSSSTVVSTQRSQDHFHVFVGDLSPEI-TTEDIKAAFAPFGRISDARVV
          IM.KEVKV.....P....K.DTSSSTVVSTQ.S..HFHVFVG..SPEI.TTEDIKAAF.PFGRIS.A.V.
Retrocopy IMSKEVKVK--QLPAVKRK<DTSSSTVVSTQYSPAHFHVFVGYFSPEI>TTEDIKAAFVPFGRISNAHVF

Parental  KDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPP-APKSTYESNTKQLSYDEVVN
          KDMATGKS.GYGFVSFFNKW..EN.I.QMG.QWLGG...RTNWA..KPP.APKST.ESNT.QLSYDEVVN
Retrocopy KDMATGKSRGYGFVSFFNKWEGENTIEQMGDQWLGG**MRTNWAMQKPP>APKSTHESNTEQLSYDEVVN

Parental  QSSPSNCTVYCGGVTSGLTEQLMRQTFSPFGQIMEIRVFPDKGYSFVRFNSHESAAHAIVSVNGTTIEGH
          .SSPS.CTVYC.GVTSGL.EQLM.QTF.PFGQIMEI..FPDK..SFVRFNSHESAA.AI.SV.GTTIE.H
Retrocopy *SSPSSCTVYCRGVTSGLREQLMHQTFLPFGQIMEICIFPDKRCSFVRFNSHESAAYAIISVIGTTIEDH

Parental  VVKC
          V.KC
Retrocopy VMKC

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_562 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
Loxodonta africana	ENSLAFG00000003463	1 retrocopy	retro_lafr_562 ,
Tupaia belangeri	ENSTBEG00000017228	1 retrocopy	retro_tbel_2567,
Tursiops truncatus	ENSTTRG00000001195	1 retrocopy	retro_ttru_1198,