RetrogeneDB ID: retro_etel_2017

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_325301:47653..48530(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000006784
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000000341
• Aliases: None
• Description: None

Sequence

>retro_etel_2017
TATAGATCTGGTGGCAGCAGTGCACCCGATGAGTTTCCGACAGACGTTCCAGGGACCAAAGGGAACTTCAAGTTAGTCAG
GCACGTTTCCTTCGTGGACTGTCCAGGCCATGAGATTTTGGTGGCTACCATGCTGAACGGGGCCACAGTGATGGATGCAG
CTCTTCTGCGGATAGCTGGTAATGAATCTTGTCCCCAGCCACAGATGTCTGAACATCTGGCTGCTATAGAAATCATGAAA
CTGAAACATATTTTGATTCTACAATATAAAATCCATTTGGTGAAAGAAAGGCAGGCTGAAGAACACTATGAACACATCCT
TGCATTTGTACAAGGTATAGGGGCAGAAGGAGTGCCGATTAGTCCGATTTCTGTTCAGCTGAAGTACAATATCGAAGTGG
TCTGTGAGTACATAGTAAAGAAATTCCATTACCTTCCAGAGACTTTACTTCAGAACCCCGACTCATTGTGATTAGGTCCT
TTGATGTCAACAAACCTGGCTGTGAGGTTGACGACCTTAAGGGGGCTGTTGCTGGAGGTAGTCTTCTAAAAGAAGTGTTA
AAGGTGGGCCAAGAGATAGAAGTCCGACCTGGTATTGCTTCCAAAGACAGTGAAGGAAAATTCATGTGCAAGCCAATCTT
TTCCATAATTGTGTCACTTTTTGTGGAGCATAATGATCTTCAGTATGTGGTTCCAGAGGGTCTTATTGGAGTTGGAACAA
AAATTGACCCCACTTTGTGCCAAGTGGACAGAATGGTCGGGCAGGTACTTGGTGCCGAAGGAGTTTTACCTGAGATCTTC
ACAGAGTTGGAAATGTCCTATTTCCTACTCAGACGGCTTCTAGGTGTACACACTGAAGAGACAAGAAAGCAGCCAAG

Alignment

ORF - retro_etel_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.44 %
• Parental protein coverage: 74.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTS
          YRS.GSS.PDEFPTD.PGTKGNFKLVRHVSFVDCPGH.IL.ATMLNGA.VMDAALL.IAGNESCPQPQ.S
Retrocopy YRSGGSSAPDEFPTDVPGTKGNFKLVRHVSFVDCPGHEILVATMLNGATVMDAALLRIAGNESCPQPQMS

Parental  EHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVK
          EHLAAIEIMKLKHILILQ.KI.LVKE.QA.E.YE.ILAFVQG..AEG.PI.PIS.QLKYNIEVVCEYIVK
Retrocopy EHLAAIEIMKLKHILILQYKIHLVKERQAEEHYEHILAFVQGIGAEGVPISPISVQLKYNIEVVCEYIVK

Parental  K-IPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLM
          K.IP.P.RDFTSEPRLIVIRSFDVNKPGCEVDDLKG.VAGGS.LK.VLKVGQEIEVRPGI.SKDSEGK.M
Retrocopy K<IPLPSRDFTSEPRLIVIRSFDVNKPGCEVDDLKGAVAGGSLLKEVLKVGQEIEVRPGIASKDSEGKFM

Parental  CKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRR
          CKPIFS.IVSLF.EHNDLQY..P.GLIGVGTKIDPTLC..DRMVGQVLGA.G.LPEIFTELE.SYFLLRR
Retrocopy CKPIFSIIVSLFVEHNDLQYVVPEGLIGVGTKIDPTLCQVDRMVGQVLGAEGVLPEIFTELEMSYFLLRR

Parental  LLGVRTE-GDKKAAK
          LLGV.TE..DKKAAK
Retrocopy LLGVHTE<RDKKAAK

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_2017 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017 ,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,