RetrogeneDB ID: retro_etel_32

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_111597:445..880(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000001072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSETEG00000010340
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_etel_32
CTTCAGATTTGGGACACGGCTGGCCAGGAGAGGTTCCGCACAATCACGCAGAGTTACTACCGCAGTGCCAACAGAGCCAT
CCTCGCATATGACATTACCAAGAGGAGCTCCTTCCTTTCCGTGCCTCACTGGATCGAGGATGTGCGGAAGTATGCAGGCT
CCAACATTGTGCAGCTGCTGATCGGGAACAAGTCGGACCTCGAGGAGCTCCGGGAGGTGCCGCTGGCCGAGGTGCAGAGC
CTGGCCGAGCACTACGACATCTTGTGTGCCATCGAGACGTCGGCCAAGGACTCGAGCAATGTGGAGGAGGCTTTCCTCCG
GGTGGCCACGGAGCTCATCGTGCGGCACGGCGGCCACATGTTCAGCGAGAAGAACACCGACCACATCCAGCTGAACACCA
AGGACGTCTCAGAGAGCTGGGGCTGTGGGTGCTGA

Alignment

ORF - retro_etel_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.36 %
• Parental protein coverage: 52.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESR
          LQIWDTAGQE.FR.IT.SYYR.A..A.L.YDIT.R..F.....W.ED.R....SN.V..LIGNKSDLE..
Retrocopy LQIWDTAGQERFRTITQSYYRSANRAILAYDITKRSSFLSVPHWIEDVRKYAGSNIVQLLIGNKSDLEEL

Parental  REVKKEEGEAFAREHGLI-FMETSAKTASNVEEAFINTAKEI
          REV...E....A.........ETSAK..SNVEEAF...A.E.
Retrocopy REVPLAEVQSLAEHYDILCAIETSAKDSSNVEEAFLRVATEL

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_32 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 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32 ,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650,