RetrogeneDB ID: retro_lafr_1241

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_90:900828..901116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19ORF70
• Ensembl ID: ENSLAFG00000026050
• Aliases: None
• Description: None

Sequence

>retro_lafr_1241
GTGTGGTCGCTGATGAGGTGTCTTATCAAAGGTGGTATGGCAGGGAGTACTGTCAACCTGGTACATGACCAGGAGGGGCT
GGGACCCAGCGACAAGAGCCAGACGGCCCTTTGGAAGGCAGAGGAGGTAGTTCCACCTGCCATGTACCAGTTCAGCCAGT
ATGTGTACAAGCAGACTGGCCTGCAGATGCGCCAGCTCTCACGCCCTTCAGAGCTTAACTTTTTCATCCTCGAGTCCTGG
AATTCAGGCATCATCACGGTGATGTCAGCTCTATTGGTGGCCCCCTCC

Alignment

ORF - retro_lafr_1241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.04 %
• Parental protein coverage: 81.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWSLMRFLIKGSVAGGAVYLVYDQDLLGPSDKSQAALRKAEEVVPPAMYQFSQYVCKQTGLQIPQLPPPP
          VWSLMR.LIKG..AG..V.LV.DQ..LGPSDKSQ.AL.KAEEVVPPAMYQFSQYV.KQTGLQ..QL..P.
Retrocopy VWSLMRCLIKGGMAGSTVNLVHDQEGLGPSDKSQTALWKAEEVVPPAMYQFSQYVYKQTGLQMRQLSRPS

Parental  KLNFSFRDSWNSGIITVMSALSVAPS
          .LNF....SWNSGIITVMSAL.VAPS
Retrocopy ELNFFILESWNSGIITVMSALLVAPS

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_1241 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706, retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329, retro_cjac_735,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241 ,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,