RetrogeneDB ID: retro_lafr_425

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:17176838..17177354(+)
• Located in intron of: ENSLAFG00000007996

Retrocopy information

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

Parental gene information

• Parental gene symbol: IL18
• Ensembl ID: ENSLAFG00000028093
• Aliases: None
• Description: None

Sequence

>retro_lafr_425
TTAGGCTTTATACCTGAAAACAATGGAAGCCTGGAATCAGATCACTTCAGCAAGCTTGAACCAACTAAATTTGCCATCAT
ATGAAATTTGAACGACCAAGCTCTCTTCATTGACCACAGAAGTAAACCTGTGTTTGAGGATATGCCTGATTCTGACTGTA
AAGATAATGTACCCCAGACCATATTTATAATAACAATGTATAAGGATAGCCAACCTAGATATCTGGCAGTAACCACCTCT
GTGAACTGTATGAAAACAATTCCTACCGTTTCCTGTGAGAACAAAACTATTGACTTTAAGGAAATCACTCCTCCTGAAGA
TATCAAGGATACACAAAGTGACATCATATTCTTTGTGAAAGGTGTTGAAGGACATGAAAAGACATAATTTGAATCTTCAT
CATACCCAGGATCCTTTCTCGCTTCTGAAAGAGATGCGGACCTTTACAAACTCATTGGGAAAAAGAAGAACCAAATTGGG
GATAGTTCTATACTGTTCACTGTAGACCTCCAAGAG

Alignment

ORF - retro_lafr_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 88.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYFIPENDGSLESDHFGKLEPTKFAIIRNLNNQVLFIDQKNKPVFEDMPDSDCNDNAAQTVFIITMYKDS
          L.FIPEN.GSLESDHF.KLEPTKFAII.NLN.Q.LFID...KPVFEDMPDSDC.DN..QT.FIITMYKDS
Retrocopy LGFIPENNGSLESDHFSKLEPTKFAII*NLNDQALFIDHRSKPVFEDMPDSDCKDNVPQTIFIITMYKDS

Parental  QPRRLAVTVSVKCSKRILTLSCENKTANFKEMSPPEDINDTQSDIIFFMKGVEGHDEKTQFESSSYPGYF
          QPR.LAVT.SV.C.K.I.T.SCENKT..FKE..PPEDI.DTQSDIIFF.KGVEGH.EKT.FESSSYPG.F
Retrocopy QPRYLAVTTSVNCMKTIPTVSCENKTIDFKEITPPEDIKDTQSDIIFFVKGVEGH-EKT*FESSSYPGSF

Parental  LASERDADLYKLILKEKNQIGDNSVMFTIDLQE
          LASERDADLYKLI.K.KNQIGD.S..FT.DLQE
Retrocopy LASERDADLYKLIGKKKNQIGDSSILFTVDLQE

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_425 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	ENSLAFG00000028093	1 retrocopy	retro_lafr_425 ,
Mustela putorius furo	ENSMPUG00000003678	1 retrocopy	retro_mputfur_732,
Pteropus vampyrus	ENSPVAG00000014063	1 retrocopy	retro_pvam_854,