RetrogeneDB ID: retro_lafr_155

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:9253035..9253927(-)
• Located in intron of: ENSLAFG00000010257

Retrocopy information

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

Parental gene information

• Parental gene symbol: LZTFL1
• Ensembl ID: ENSLAFG00000010237
• Aliases: None
• Description: None

Sequence

>retro_lafr_155
GCAGAGTTGGGCCTAAATGACCACCATTAATATGAAGTTATTAATTATATGCATTTTGCTTGTTCAAAAAGAGGCTTGAG
ACACAAAACGGTAGACTCTTGCTTCCAAGACCTCAAGGAGAGCAGGCCGGGGAGGAGACCTTCAGCATTGATGAGGTCTC
TGAGGTCCTGCGGGGATTACAAGCTGCAGTTCACAGTGAGGCGGAGTCTGAGCTCATCAACACTGCCTACACCAGTGTGT
TACTTCTGCAGCAGCTTTTTTCACAAGCTGAGAAGTGGTATCTTAAGCTATAGACAGACATCTCTGATGTCTGAAAACAG
AATTATTAGAACAAGTTGCAGAATTTGAAAAGACAGAGTTTACATCTTCAGACAAAAAGCCTGCTTTAGAAATCATAAAA
TCAAAACTTGCTCTGCTTAATGAAAGCAGAATAGCAAAATTCCTAAACAAGGAAATTCTGAGGCTTCAAGAAGAGAATGA
GAAATTGAAGTCAAAGCTGAAGACCAATGAAATACAGGCTACAAATGCATTGGATGAGAAGTCCAAACTAGAAAGAGCGC
TGAGAGATTTACAGCTTGATCAAGGAAATCAAAAGGATTTTATAAAGGCCCAACACGAGTGAGTTAGAAAAAACATGGCC
GCTGCTTTAAAGAGTGAGTTTCAGAGGACACTCAGTGACAAGATAGAGAACCAGAAGTCCCTGGAGGAGAATGTAGCAAC
AGCCAAGTCTGACCTACTCCTGGTTCAAGAGCAGCTGAGCTTGGCTGAAAAGGATTTGGAAAAGAAATTCCAACAAACAG
CCACTTACTGAAATATGAAAGAGATTCCTACCAAGAAGAATGACCTGATCAAGGAGCTAAGGAAATGACTGGCAAAATAC
AAACCTGAAGAA

Alignment

ORF - retro_lafr_155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AELGLNDHHQNEVINYMRFARSKRGLRLKTVDSCFQDLKESR-LVEETFTVDEVSEVLSGLQAVVHSEVE
          AELGLNDHH..EVINYM.FA.SKRGLR.KTVDSCFQDLKESR...EETF..DEVSEVL.GLQA.VHSE.E
Retrocopy AELGLNDHH*YEVINYMHFACSKRGLRHKTVDSCFQDLKESR<AGEETFSIDEVSEVLRGLQAAVHSEAE

Parental  SELINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENR-ELLEQVAEFEKAEFTSSNKKPLLDAVKPKLA
          SELINTAYT.VLLL.QLFSQAEKWYLKL.TDIS......ELLEQVAEFEK.EFTSS.KKP.L...K.KLA
Retrocopy SELINTAYTSVLLLQQLFSQAEKWYLKL*TDISDV*KQ<ELLEQVAEFEKTEFTSSDKKPALEIIKSKLA

Parental  PLNEGGTAELLNKEILRLQEENEKLKSRLKTIEIQVTNTLDEKSKLERALRDLQLDQGAEKDFIKAQDLS
          .LNE...A..LNKEILRLQEENEKLKS.LKT.EIQ.TN.LDEKSKLERALRDLQLDQG..KDFIKAQ...
Retrocopy LLNESRIAKFLNKEILRLQEENEKLKSKLKTNEIQATNALDEKSKLERALRDLQLDQGNQKDFIKAQHE*

Parental  ELENTVAALKSEFERTLTDKTENQKSLEENLATAKHDLLRVQEQLSLAEKELEKKFQQTAAYRNMKEILT
          ...N..AALKSEF.RTL.DK.ENQKSLEEN.ATAK.DLL.VQEQLSLAEK.LEKKFQQTA.Y.NMKEI.T
Retrocopy VRKNMAAALKSEFQRTLSDKIENQKSLEENVATAKSDLLLVQEQLSLAEKDLEKKFQQTATY*NMKEIPT

Parental  KKNDQIKELRKKLAKYEPED
          KKND.IKELRK.LAKY.PE.
Retrocopy KKNDLIKELRK*LAKYKPEE

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_155 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003899	1 retrocopy	retro_chof_1935,
Echinops telfairi	ENSETEG00000013761	1 retrocopy	retro_etel_1726,
Loxodonta africana	ENSLAFG00000010237	1 retrocopy	retro_lafr_155 ,
Mus musculus	ENSMUSG00000025245	3 retrocopies	retro_mmus_1834, retro_mmus_3266, retro_mmus_3276,
Procavia capensis	ENSPCAG00000009783	1 retrocopy	retro_pcap_313,