RetrogeneDB ID: retro_etel_1523

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_276854:45272..46694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAREM
• Ensembl ID: ENSETEG00000015863
• Aliases: None
• Description: GRB2 associated, regulator of MAPK1 [Source:HGNC Symbol;Acc:26136]

Sequence

>retro_etel_1523
GAATGCATAGTAGGCCTGCAGGAGAACGACTACCTTCTGATTCATTCATGCCGTCAGTGGACGACCATCACTGCCCATAG
TTTGGAGGAGGGGCACTATGTCATTGGGCCTAAGATAGAGATTCTGGTACATTATACAGGACAATTTAAACTGCTGGAGC
AGGGCCGAGATATAAAGGAGCCAGTGCAATATTTTAACAGTGTAGAGGAGGTGGCTAAAGCATTTCCTGAACGCGTGTAC
ATCATGGAGGAAATAACATTCAATGTTAAGGTTGCTGCAGGAGAATGTAATGAAGACACGGAAGTTTACAACATCACCCT
CTGTACTGGGGACGAACTCAGGCTCATGGGCCAGGCGGAAATCCTCTATGTTTAGACTTTCAAGGAAAAATCTCCACTCA
ACAAGATCTTCAAAAAGATCGGGAACTCAATTCCATCAGCAACCTGGGTAAAGGCAAAATGCAGTGCCTCATTTGCATGA
ACCACCTGACCAAGGAGAGCAACAGCCTCCCATTCCAGTTCAAGGACCCATATAGCACTCGGAGTCCCCTGGAGCTTCAG
ATGCAAGAGAATGAGCACACTATCCGCAACATTGTGGAGAAAACCAGGCTCCATGTGAACATGATCATGCCGAGACCCCC
ACCGAGAAACGTGTATGACCTCCACTTCATCCGCAAGGGTCACTGCTACAAGACCAAGACCGTGGTGGTTTGCTGTGTGC
TGCGGAGCACCAAGATCTTCCCCATACACTTCCCTTTGCACTTTACTGTTCTGAGGTTTAGCCTCTCATAACACCTGGTG
AAGGGCAAGATATGGCCCGAAACCTTGACCCATCATTGTCTGGGCATCTGCGAAGAACAGTTCGACATTGATTAGTATTC
ACGGGCTGTCCATGATGTGAAGACGGACTGGAACGAGGACTGCAAGAGCCCCACGAAGGGCCAGTGCTCTGACCACAATC
ATGTGCCCAATTCCCTCAGCTATGCCCAGGAGGAGCTCACCCAGTCGTTCCACTGGCTCTCAGTCTGTGTGTATGACAAC
AATCTCCGTGGCAACAGTGAAGTGAACCTCCACGGCTGCAGAGACTTGGGGGGAGAGTGGGCCCCTTTCCCTAATGACAT
CCTTCCCTACCAGGACCATGGTGACAGTAGAGCAACCACCTTTTCCCAGAACCTAGTAAAGAATCCGCAGGTGTCCTCAG
CAAGCCAGAACTTCCTCATGAGGAGCTGTGACTGGATGACGGCAAGACCAGCCATGCACCTCTCACCCGATCCGTGAGCG
AGAAGAGCAGATGTGACCATTTCAGAAGTTTGTACGGTCCAAATATGGGACTTCTCTTCCCGTCCCTGGGACTCTGGGAG
CATCAATGAAGTCTTCAGATATCACCCTCCCTCAGCCTCCAGTGCCTCCCAAATCTAAAGCC

Alignment

ORF - retro_etel_1523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECIEGLRENDYLLIHSCRQWTTITAHSLEEGHYVIGPKIEIPVHYAGQFKLLEQDRDIKEPVQYFNSVEE
          ECI.GL.ENDYLLIHSCRQWTTITAHSLEEGHYVIGPKIEI.VHY.GQFKLLEQ.RDIKEPVQYFNSVEE
Retrocopy ECIVGLQENDYLLIHSCRQWTTITAHSLEEGHYVIGPKIEILVHYTGQFKLLEQGRDIKEPVQYFNSVEE

Parental  VAKAFPERVYVMEEITFNVKVASGECNEDTEVYNITLCTGDELTLMGQAEILYAKTFKEKSRLNTIFKKI
          VAKAFPERVY.MEEITFNVKVA.GECNEDTEVYNITLCTGDEL.LMGQAEILY..TFKEKS.LN.IFKKI
Retrocopy VAKAFPERVYIMEEITFNVKVAAGECNEDTEVYNITLCTGDELRLMGQAEILYV*TFKEKSPLNKIFKKI

Parental  G-KLNSISKLGKGKMPCLICMNHRTNESISLPFQCKGRFSTRSPLELQMQEGEHTIRNIVEKTRLPVNVT
          G..LNSIS.LGKGKM.CLICMNH.T.ES.SLPFQ.K...STRSPLELQMQE.EHTIRNIVEKTRL.VN..
Retrocopy G<ELNSISNLGKGKMQCLICMNHLTKESNSLPFQFKDPYSTRSPLELQMQENEHTIRNIVEKTRLHVNMI

Parental  VPSPPPRNPYDLHFIREGHRYKFVNIQTKTVVVCCVLRSNKILPMHFPLHLTVPKFSLPEHLVKGEVWSE
          .P.PPPRN.YDLHFIR.GH.YK........VV.C.VLRS.KI.P.HFPLH.TV..FSL..HLVKG..W.E
Retrocopy MPRPPPRNVYDLHFIRKGHCYKTKTV----VVCC-VLRSTKIFPIHFPLHFTVLRFSLS*HLVKGKIWPE

Parental  TLVHHWLGICQEQFDIDEYSRAVRDVKTDWNEDCKSPKKGRCSGHNHVPNSLSYARDELTQSFHRLSVCV
          TL.HH.LGIC.EQFDID.YSRAV.DVKTDWNEDCKSP.KG.CS.HNHVPNSLSYA..ELTQSFH.LSVCV
Retrocopy TLTHHCLGICEEQFDID*YSRAVHDVKTDWNEDCKSPTKGQCSDHNHVPNSLSYAQEELTQSFHWLSVCV

Parental  YGNNLHGNSEVNLHGCRDLGGEWAPFPNDILPYQDHGDSG-SDYLFPEPSEESAGVLGKPELPYEELWLD
          Y.NNL.GNSEVNLHGCRDLGGEWAPFPNDILPYQDHGDS..S..LFPEPS.ESAGVL.KPELP.EEL.LD
Retrocopy YDNNLRGNSEVNLHGCRDLGGEWAPFPNDILPYQDHGDSR<SNHLFPEPSKESAGVLSKPELPHEEL*LD

Parental  EGKTSHAPLTRSLSEKGRCDHFRS-SVRSKCGTSPLPAPGALGAPMKSSDVTLPPPPVPPKSEA
          .GKTSHAPLTRS.SEK.RCDHFRS..VRSK.GTS.LP.PG.LGA.MKSSD.TLP.PPVPPKS.A
Retrocopy DGKTSHAPLTRSVSEKSRCDHFRS<FVRSKYGTS-LPVPGTLGASMKSSDITLPQPPVPPKSKA

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_1523 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015863	1 retrocopy	retro_etel_1523 ,