RetrogeneDB ID: retro_lafr_862

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_41:4664163..4665524(+)
• Located in intron of: ENSLAFG00000015062

Retrocopy information

• Ensembl ID: ENSLAFG00000029209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LIN9
• Ensembl ID: ENSLAFG00000002421
• Aliases: None
• Description: None

Sequence

>retro_lafr_862
AAGAAATTTACAGCAACAATGTCAACACCAGATAAGAAATCCTCACAGAAGATTGGTTTTCGAGTACATAACCTGCTCGA
GCTTCCCAAAGCACATAAATGGTGCGTATACGAATGGTTCTACTCAAACATAGATAAACCACTTTTTGAAGGCGATAATG
ACTTTTGTGTATGTCTAAAAGAATGTTTTCCTAATTTGAAGACAAGAAAGTTAACGAGTAGAATGGGGAAAAATCAGGCG
GCTTATGGGAAAACCACGGAGATGTTCTTCTGCGTTTTTTGAGGAAGAGAGATCAGCATTAAAACAGAAACGGCAGAAAA
TAAGACTGTTACAACAAAGGAAAATTGCAGATGTTTCACAATTCAAAGATCTCCTGGAAGAAATTCCTTTGCCCCTGGTT
ATTGGAACCAAAGTTATGGCGCGGTTACATGGTGTTCACGATGGTCTGGTTCGCTGGACAAATAGATGCTGTGGATACTC
TTAGTGCTACTTACAGAGTGACTTTTGATAGGGCAGGGCTTGGAACCCATACCATCCCTGACTATGAAGTCCTTAGTAAT
GAGCCTCATGAGACAATGCCAATTGCTGTCTTTGGACAAAAACAGCGGCCTTCTCAATTTTTTATGACCCCGCCACGGTT
ACATTATACTCCTCCTCTCCAGTCACCTATTACAGATAATGATCCTTTATTAGGACAGTCACCTTGGAGAAATAAAATTT
CTGGCTCTGACACTGAAACGTTAGGTGGTTTTCCAGTAGAATTCCTTATCCAAGTGACCAAATTATCCAAAATTCTCATG
ATTAAGAAGGAACACATCAAGAAATTAAGGGAAGTGAATACAGAAGCAGAAAAATTGAAATCGTATTCCATGTCCATCAG
CACTGAATTTCAGCGAAGATATGCAACCATTGTTCTGGAGCTTGAACAGCTAAACAAAGACCTCAACAAAGTTTTGCATA
AAGTTCAGCAGTACTGCTATGAGCTTGCTCCAGATCAGGGCCTCCAGCCTGCAGGTCAGCCAACAGATATGAGACGAAGG
TCTGAAGAAGAAGCACAGGAAATTGTTTGGCATGCAGACTCCTCAACAGGACAGCCCTGTGTTGAAAATGAAAACCTTAC
AGACTTAATCTCTAGACTTACAGCTATTTTATTACAAATTAAGTGTCTTGCAGAAGGAGACCTGAATTCCTTTGAATTCA
AATCACTTACAGATTCATTAAATGATATCAAGAGTACAGTAGATGCTTCTAATATCAGCTACTTTCAGAATAATGTAGAA
ATTCGTGTTGCACATATTCAGAGTGGCTTGAGCCAGATGGGAAACTTACATGTCTTTGCAGCAAATAACACTAGCAGAGA
C

Alignment

ORF - retro_lafr_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.48 %
• Parental protein coverage: 83.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QKFTATMSTPDKKASQKIGFRLRNLLKLPKAHKWCIYEWFYSNIDKPLFEGDNDFCVCL-KESFPNLKTR
          .KFTATMSTPDKK.SQKIGFR..NLL.LPKAHKWC.YEWFYSNIDKPLFEGDNDFCVCL.K..F......
Retrocopy KKFTATMSTPDKKSSQKIGFRVHNLLELPKAHKWCVYEWFYSNIDKPLFEGDNDFCVCL<KRMFS*FEDK

Parental  KLT-RVEWGKIRRLMGKPRRCSSAFFEEERSALKQKRQKIRLLQQRKVADVSQFKDLPEEIPLPLVIGTK
          K...RVEWGKIRRLMGKPRRCSSAFFEEERSALKQKRQKIRLLQQRK.ADVSQFKDL.EEIPLPLVIGTK
Retrocopy KVN<RVEWGKIRRLMGKPRRCSSAFFEEERSALKQKRQKIRLLQQRKIADVSQFKDLLEEIPLPLVIGTK

Parental  VTARLRGVHDGL-FTGQIDAVDTLNATYRVTFDRAGLGTHTIPDYEVLSNEPHETMPIAAFGQKQRPSRF
          V.ARL.GVHDGL.F.GQIDAVDTL.ATYRVTFDRAGLGTHTIPDYEVLSNEPHETMPIA.FGQKQRPS.F
Retrocopy VMARLHGVHDGL>FAGQIDAVDTLSATYRVTFDRAGLGTHTIPDYEVLSNEPHETMPIAVFGQKQRPSQF

Parental  FMTPPRLHYTPPLQSPITDNDPLLGQSPWRNKISGSDTETLGGFPVEFLIQVTKLSKILMIKKEHIKKLR
          FMTPPRLHYTPPLQSPITDNDPLLGQSPWRNKISGSDTETLGGFPVEFLIQVTKLSKILMIKKEHIKKLR
Retrocopy FMTPPRLHYTPPLQSPITDNDPLLGQSPWRNKISGSDTETLGGFPVEFLIQVTKLSKILMIKKEHIKKLR

Parental  EMNTEAEKLKSYSMPISIEFQRRYATIVLELEQLNKDLNKVLHKVQQYCYELAPDQGLQPAGQPTDMRRR
          E.NTEAEKLKSYSM.IS.EFQRRYATIVLELEQLNKDLNKVLHKVQQYCYELAPDQGLQPAGQPTDMRRR
Retrocopy EVNTEAEKLKSYSMSISTEFQRRYATIVLELEQLNKDLNKVLHKVQQYCYELAPDQGLQPAGQPTDMRRR

Parental  CEEEAQEIVRHANSSTGQPCVENENLTDLISRLTAILLQIKCLAEGGDLNSFEFKSLTDSLNDIKSTIDA
          .EEEAQEIV.HA.SSTGQPCVENENLTDLISRLTAILLQIKCLAE.GDLNSFEFKSLTDSLNDIKST.DA
Retrocopy SEEEAQEIVWHADSSTGQPCVENENLTDLISRLTAILLQIKCLAE-GDLNSFEFKSLTDSLNDIKSTVDA

Parental  SNISCFQNNVEIHVAHIQSGLSQMGNLHAFAANNTNRD
          SNIS.FQNNVEI.VAHIQSGLSQMGNLH.FAANNT.RD
Retrocopy SNISYFQNNVEIRVAHIQSGLSQMGNLHVFAANNTSRD

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_862 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	ENSLAFG00000002421	1 retrocopy	retro_lafr_862 ,
Mustela putorius furo	ENSMPUG00000004573	1 retrocopy	retro_mputfur_1474,
Rattus norvegicus	ENSRNOG00000023304	1 retrocopy	retro_rnor_1047,