RetrogeneDB ID: retro_etel_1692

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_287875:28954..29791(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAD5
• Ensembl ID: ENSETEG00000019912
• Aliases: None
• Description: SMAD family member 5 [Source:HGNC Symbol;Acc:6771]

Sequence

>retro_etel_1692
ATTCTCCCTCCAGTGCTGGTTCCAAGACACAGCGAATATAACCCTCAGCACAGCCTGTTAGCTCAGTTCCGAAACATAGG
ACAAAATGAGCCTCACATGCCACTCAATGCCACTTTTCCAGATTCTTTCCAGCAGCCTAATAGCCATCCGTTTCCTCACT
CACCCGACAGCAGTTACCCAAACTCTCCTGGGAGCAGCAATAGCACCTACCCCCACTCTCCCACCAGCTCAGATCCCGGA
AGCCCTTTTCAGATTCCAGCTGATACACCCCCACCTGCTTACCTGCCTCCTGAAGACCCCATGGCCCAGGATGGCTCACA
GCCGATGGACACAAATATGATGGCACCTTCACTGCCCTCAGAAACCAACAGAGGAGATGCTCAGGCAGTTGCTTATGAGG
AACCCAAACATTGGTGCTCCATTGTCTACTATGAGCTCAACAATCGTGTGGGTGAAGCGTTCCATGCTTCCTCCACAAGC
GTGCTGGTGGACGGATTCACTGATCCTTCCAACATCAAGAACCGTTTCTGTCTTGGGCTGTTATCCAATGTTAACCGGAT
TTCCACTATTGAAAACACGAGGCGGCACATTGGAAAAGGCGTCCATCTGTATTACGTTGGTGGAGAGGCGTATGCCGAGT
GCCTCAGTGACAGTAGCATCTTTGGGCAAAGTCGGAACTGCAACTACCACCATGGATTCCATCCCACTACCGTGTGCAAG
ATCCCTAGTGGGTGTAGTCTGAAAATTTTCAACAACCAAGAATTCGCTCAGTTACTGGCACAGTCCGTGAACCATGGTTT
CGAGACCGTCTACGAGCTCACCAAAATGTGTACAGTA

Alignment

ORF - retro_etel_1692 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 66.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLPPVLVPRHNEFNPQHSLLVQFRNLSHNEPHMPQNATFPDSFHQPNNTPFPLSPNSPYPPSPASS--TY
          .LPPVLVPRH.E.NPQHSLL.QFRN...NEPHMP.NATFPDSF.QPN..PFP.SP.S.YP.SP.SS..TY
Retrocopy ILPPVLVPRHSEYNPQHSLLAQFRNIGQNEPHMPLNATFPDSFQQPNSHPFPHSPDSSYPNSPGSSNSTY

Parental  PNSPASSGPGSPFQLPADTPPPAYMPPDDQLGPDNSQPMDTSNNMIPQIMPSISSRDVQPVAYEEPKHWC
          P.SP.SS.PGSPFQ.PADTPPPAY.PP.D....D.SQPMDT.N.M.P.........D.Q.VAYEEPKHWC
Retrocopy PHSPTSSDPGSPFQIPADTPPPAYLPPEDPMAQDGSQPMDT-NMMAPSLPSETNRGDAQAVAYEEPKHWC

Parental  SIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHIGKGVHLYYVGGE
          SIVYYELNNRVGEAFHASSTSVLVDGFTDPSN.K.RFCLGLLSNVNR.STIENTRRHIGKGVHLYYVGGE
Retrocopy SIVYYELNNRVGEAFHASSTSVLVDGFTDPSNIKNRFCLGLLSNVNRISTIENTRRHIGKGVHLYYVGGE

Parental  VYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEFAQLLAQSVNHGFEAVYELTKMCTI
          .YAECLSDSSIF.QSRNCN.HHGFHPTTVCKIPS.CSLKIFNNQEFAQLLAQSVNHGFE.VYELTKMCT.
Retrocopy AYAECLSDSSIFGQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTV

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_1692 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019912	1 retrocopy	retro_etel_1692 ,
Oryctolagus cuniculus	ENSOCUG00000004937	1 retrocopy	retro_ocun_767,