RetrogeneDB ID: retro_lafr_896

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_45:16197983..16198219(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMC2
• Ensembl ID: ENSLAFG00000004378
• Aliases: None
• Description: None

Sequence

>retro_lafr_896
GTGCATCCTGACTTATCCTCACACTTGCACACCGAAGAACGCAGCATCTTGATTAACTTGCTAAAGGAATGTCACAAAAA
CCACAGCTTTCTGAAATTTTTTGGTCGTTGCAATGATCTTGATCGGCGGATAGAAAATGCCTGAAGAACGAGTACGTGGA
GAAGAGGACCAAGAGCAGGGAGCATGGAAATGCGACGTGAGAGGGACCTTTTAATCCTCCAGAAGAGTTTGAAAAA

Alignment

ORF - retro_lafr_896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHPDLSPHLHTEECNILINLLKECHKNHSFLKFFGHCNDLDRQM-RKCLKKEYVEKRAKSRERGDAMRKR
          .HPDLS.HLHTEE..ILINLLKECHKNHSFLKFFG.CNDLDR...RKCLK.EYVEKR.KSRE.G.A....
Retrocopy VHPDLSSHLHTEERSILINLLKECHKNHSFLKFFGRCNDLDRRI<RKCLKNEYVEKRTKSREHGNAT*EG

Parental  LFNPPQESEK
          .FNPP.E.EK
Retrocopy PFNPPEEFEK

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_896 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013929	2 retrocopies	retro_amel_397, retro_amel_681,
Bos taurus	ENSBTAG00000017009	1 retrocopy	retro_btau_109,
Echinops telfairi	ENSETEG00000010422	3 retrocopies	retro_etel_2190, retro_etel_357, retro_etel_816,
Felis catus	ENSFCAG00000004977	1 retrocopy	retro_fcat_193,
Loxodonta africana	ENSLAFG00000004378	2 retrocopies	retro_lafr_311, retro_lafr_896 ,
Microcebus murinus	ENSMICG00000011915	2 retrocopies	retro_mmur_1149, retro_mmur_701,
Monodelphis domestica	ENSMODG00000025763	1 retrocopy	retro_mdom_1670,
Sorex araneus	ENSSARG00000008906	2 retrocopies	retro_sara_712, retro_sara_84,
Sarcophilus harrisii	ENSSHAG00000001006	1 retrocopy	retro_shar_254,
Tupaia belangeri	ENSTBEG00000000038	3 retrocopies	retro_tbel_1840, retro_tbel_1979, retro_tbel_2249,