RetrogeneDB ID: retro_etel_1418

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_262838:8512..9151(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFR1
• Ensembl ID: ENSETEG00000015444
• Aliases: None
• Description: SWI5-dependent recombination repair 1 [Source:HGNC Symbol;Acc:29574]

Sequence

>retro_etel_1418
AGAATTCAAGGCTTCACGTTTAAGATGGAAAGGCCGTCAGATCCAGTGTTGATGTCACCCAGTATGCCACAGGCCTGTGA
GATCCCGCCATTTCCCCATACTCATAGTTCAGGCAAGCAACCTATGAGTGCAACACTGAGGGAACGATTAAGAAAAACAA
GATCATCTGTTCATTTCTGTTACAGGGCCGTGGTAAAACGCCTTAAAGTAGAGGAAGAAGAAAGAGATAGAGTTTCTCAG
ACAAGTCTATCTCCTCCACAGATGAAAACTGTTTTGGGTTTCAAGAAAGTGTGAAGCACAGAGGCCGCTTAGTGGGAAGG
AATTACGTACTTGAACAATGCCATCGAGGACATCAGTGCACGTGATGCTACGCGCCTTGATGGTGGGCCGAGCAGTGCTC
CCTCCCAAAATGATTCTGTCCATGAGAACCTTCCCACCCGAGGCAGAGTACAGGGAGCAAGAGCAACGTTGGTGAAGCAG
GTTCAGGAGAAAGAAGACTTTCTTCAGAGGCTGAAACTAGTCAAAATGTATAGATCCAAGAATGACCTAGCTCAGATCCG
GTTGCTGATAAAGAAGTGGAGAAGCTGTAGCCAGCTGGTGCTTTATGAGTTGCAGTCAGGTATGTCTGGAGAACAAGAA

Alignment

ORF - retro_etel_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.93 %
• Parental protein coverage: 69.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RIQGFTLKMERPSDPALTSPTTPQACEIPPSPHTHSSGKQPMSATLRERLRKTRSSFHSCYSTVVKRLKV
          RIQGFT.KMERPSDP.L.SP..PQACEIPP.PHTHSSGKQPMSATLRERLRKTRSS.H.CY..VVKRLKV
Retrocopy RIQGFTFKMERPSDPVLMSPSMPQACEIPPFPHTHSSGKQPMSATLRERLRKTRSSVHFCYRAVVKRLKV

Parental  EDEERDE-SFSDKSISSTDENCLGFQESVKHRGRE-FEESTYLNSAIQDISARDATPLDGGPSSA-RQNT
          E.EERD..SFSDKSISSTDENC.GFQESVKHRGR...E..TYLN.AI.DISARDAT.LDGGPSSA..QN.
Retrocopy EEEERDR<SFSDKSISSTDENCFGFQESVKHRGRL>WEGITYLNNAIEDISARDATRLDGGPSSAPSQND

Parental  SVHENLPSPGGGREERAMLVKQIQEKEDFLRRLKLVKMYRSKNDLSQIQLLIKKWRSCSQLVLYELQSAM
          SVHENLP..G.....RA.LVKQ.QEKEDFL.RLKLVKMYRSKNDL.QI.LLIKKWRSCSQLVLYELQS.M
Retrocopy SVHENLPTRGRVQGARATLVKQVQEKEDFLQRLKLVKMYRSKNDLAQIRLLIKKWRSCSQLVLYELQSGM

Parental  SEENK
          S.E..
Retrocopy SGEQE

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_1418 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005386	2 retrocopies	retro_ecab_726, retro_ecab_887,
Echinops telfairi	ENSETEG00000015444	1 retrocopy	retro_etel_1418 ,
Gorilla gorilla	ENSGGOG00000025713	1 retrocopy	retro_ggor_3039,
Macaca mulatta	ENSMMUG00000015327	1 retrocopy	retro_mmul_2606,
Pteropus vampyrus	ENSPVAG00000004202	1 retrocopy	retro_pvam_742,