RetrogeneDB ID: retro_etel_1721

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_289922:43020..43272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSETEG00000018837
• Aliases: None
• Description: autophagy related 12 [Source:HGNC Symbol;Acc:588]

Sequence

>retro_etel_1721
ATCTTTCTAAAGTCTGTGGGAGAAACCCCTATTACGAAAACAAAGAAGTGGGCTCTAGAGCGAACCTGAACTATCCAAGC
ACTCATAGAATGTATTAAAAAGTTCCCTAAACTAGTGGCCTCCAAAAGTTTATTTGTTTATATGAATCAGTCCTTTGCCC
TTTCCCCAGATCAGGAAGTTGGAACACTGTATGAATGTTTAGGTAATTATGGTAAACTGGTCTTACATTACTACAAGTCC
CAGGCTTGTGGT

Alignment

ORF - retro_etel_1721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSD
          I.LK.VG.TPI.KTKKWA.ERT.TIQ.LI..IKKF.KLVAS..LF.Y.NQSFA.SPDQEVGTLYEC.G..
Retrocopy IFLKSVGETPITKTKKWALERT*TIQALIECIKKFPKLVASKSLFVYMNQSFALSPDQEVGTLYECLGNY

Parental  GKLVLHYCKSQAWG
          GKLVLHY.KSQA.G
Retrocopy GKLVLHYYKSQACG

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_1721 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721 ,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,