RetrogeneDB ID: retro_etel_220

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_3759:90132..90580(-)
• Located in intron of: ENSETEG00000019708

Retrocopy information

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

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSETEG00000016758
• Aliases: None
• Description: APAF1 interacting protein [Source:HGNC Symbol;Acc:17581]

Sequence

>retro_etel_220
GGAATTAGCTTGAAGCATGGAAATGAAATCTATATCACCCCTTGCAGGAGTGCAAAAGGAGTGAATTCAGCCTGAGGACC
TGTTTGTTTGTGACAAGAATGAATAGGACCTAAGTGGGCCTCCGCCATCTAACATGCTCAGGAAAGCCAGTGTATCCTCT
TTCATAAATGCTTACACAATGAGAGGAGCCAGTGTAGTGATCCACACCCACTCTCAAGCTGCTGTCATGGCCACCCTCCT
TTTTCCAGGACAAGAGTTTAAAATTACACATCAGGAGATGATGAAAGGAATAAGGAAGTGTACCTCAGGAGGGTATTATC
GAAACAGTGCTCTGTTGGTAGTGCCCATTATTGAGAATACACCTGAGGAGAAAGACCTCTAAAAACAAATGGCTCGTGCA
ATGGATGAGTACCCAGACTCCTGTGCGATGCTGCTCAGAGGACACGGG

Alignment

ORF - retro_etel_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 70.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GISLKHGNEIYIAP-SGVQKERIQPEDLFVCDINEQDIRGPPPHKQLSKSQCTPLFMNAYTMRGAGAVIH
          GISLKHGNEIYI.P..GVQKE.IQPEDLFVCD.NE.D..GPPP...L.K......F.NAYTMRGA..VIH
Retrocopy GISLKHGNEIYITP>AGVQKE*IQPEDLFVCDKNE*DLSGPPPSNMLRKASVSS-FINAYTMRGASVVIH

Parental  THSKAAVLATLLFPGQEFKITHQEMIKGIRKGTSGGYYRYDDMLVVPIIENTPEEKDLKERMARAMDEYP
          THS.AAV.ATLLFPGQEFKITHQEM.KGIRK.TSGGYYR....LVVPIIENTPEEKDL...MARAMDEYP
Retrocopy THSQAAVMATLLFPGQEFKITHQEMMKGIRKCTSGGYYRNSALLVVPIIENTPEEKDL*KQMARAMDEYP

Parental  DSCAVLVRRHG
          DSCA.L.R.HG
Retrocopy DSCAMLLRGHG

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_220 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016758	1 retrocopy	retro_etel_220 ,
Homo sapiens	ENSG00000149089	1 retrocopy	retro_hsap_4208,
Gorilla gorilla	ENSGGOG00000022940	2 retrocopies	retro_ggor_2818, retro_ggor_2873,
Ornithorhynchus anatinus	ENSOANG00000007394	6 retrocopies	retro_oana_108, retro_oana_109, retro_oana_121, retro_oana_63, retro_oana_85, retro_oana_96,
Pongo abelii	ENSPPYG00000003361	1 retrocopy	retro_pabe_3442,
Pan troglodytes	ENSPTRG00000003499	1 retrocopy	retro_ptro_2856,
Sarcophilus harrisii	ENSSHAG00000011523	1 retrocopy	retro_shar_574,
Ictidomys tridecemlineatus	ENSSTOG00000004390	1 retrocopy	retro_itri_1029,