RetrogeneDB ID: retro_etel_1497

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_274817:10045..10469(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSETEG00000008047
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit I [Source:HGNC Symbol;Acc:3272]

Sequence

>retro_etel_1497
CTGCGGGAGTGCATCAGCGCTGGCCATGAGAGCAGAGAGCTCAACCAGTACAGCGCCAGGTCTGGAGAGGTGCTAGTGAA
TGTGAAGGAGCACTCGAGGCAGATCAATGACAGCCAGCTATCCAGGGGCATGACCATGTTCGTCACCGCATCCAAGGGCA
ACACATCCAAGCTCGTTGACGCCACAACCCTCCAACACCAGAACCTTTCCGGACAGAGCATCCTGTCAACGCAGCTGCCC
TTTCTCCCAACTATGACCACGTGGTGCTGGGGGTGGTCAGGAAGCCATGGATGTCACCACAACCTCCACCAGGATTGGCA
AGTTTGAAGCCAGGTTCTTCCATTTGGCCTTTGAAGAGGAGTTTGGAAGAACCAAGGGTCACTTTGGTCCTATCAACAGG
GTGGCCTTCCACCCTGGTGGCCAG

Alignment

ORF - retro_etel_1497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 66.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGECIIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDNTSKLFDSTTLKHQ-KT
          L.ECI.AGHES.ELNQYSA.SGEVLVNVKEHSRQIND.QLSR.MTMFVTASK.NTSKL.D.TTL.HQ...
Retrocopy LRECISAGHESRELNQYSARSGEVLVNVKEHSRQINDSQLSRGMTMFVTASKGNTSKLVDATTLQHQ<EP

Parental  FRTERPVNSAALSPNYDHVVL-GGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRIKGHFGPINSVAFH
          FRTE.PVN.AALSPNYDHVVL.GGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGR.KGHFGPIN.VAFH
Retrocopy FRTEHPVNAAALSPNYDHVVL<GGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRTKGHFGPINRVAFH

Parental  PDGK
          P.G.
Retrocopy PGGQ

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_1497 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497 ,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548,