RetrogeneDB ID: retro_etel_1766

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_292682:9859..10156(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP1LC3A
• Ensembl ID: ENSETEG00000012407
• Aliases: None
• Description: microtubule-associated protein 1 light chain 3 alpha [Source:HGNC Symbol;Acc:6838]

Sequence

>retro_etel_1766
GTGCAGCAGATCCGCGACCAGCTCCCCAGCAAGATCCCGGTGATCATCGGACGCTACAAGCGGGAGAAGCAGCTGCCAGT
CCCGGATAAGACCAAGTCCCTGGTCCCAGACCACGTCAACACGAGCAAGCTGGTCCAGATCATCCGGCGCCGCCTGCAGC
TGAGCGCCACGCAGGCTTTCTTCCTGCTCGTGAACCAGCACAGCACGGTCAGCGTGTCCACGCCCATCGCCCACATCTAT
GATCCGGAGACGAACGAGGATGGTTGCCTCTATATGGTCTACGCCTCCCAGGAAACC

Alignment

ORF - retro_etel_1766 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 92.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMV
          VQQIRDQ.PSKIPVII.RYK.EKQLPV.DKTK.LVPDHVN.S.LV.IIRRRLQL..TQAFFLLVNQHS.V
Retrocopy VQQIRDQLPSKIPVIIGRYKREKQLPVPDKTKSLVPDHVNTSKLVQIIRRRLQLSATQAFFLLVNQHSTV

Parental  SVSTPIADIYEQEKDEDGFLYMVYASQET
          SVSTPIA.IY..E..EDG.LYMVYASQET
Retrocopy SVSTPIAHIYDPETNEDGCLYMVYASQET

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1766 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562, retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Echinops telfairi	ENSETEG00000012407	1 retrocopy	retro_etel_1766 ,
Echinops telfairi	ENSETEG00000015189	2 retrocopies	retro_etel_1050, retro_etel_3,
Felis catus	ENSFCAG00000022040	1 retrocopy	retro_fcat_1634,
Monodelphis domestica	ENSMODG00000002694	1 retrocopy	retro_mdom_1256,
Mustela putorius furo	ENSMPUG00000017814	1 retrocopy	retro_mputfur_1049,
Ictidomys tridecemlineatus	ENSSTOG00000006158	2 retrocopies	retro_itri_287, retro_itri_988,