RetrogeneDB ID: retro_etel_1220

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_230646:3365..4381(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010796
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FXR2
• Ensembl ID: ENSETEG00000018613
• Aliases: None
• Description: fragile X mental retardation, autosomal homolog 2 [Source:HGNC Symbol;Acc:4024]

Sequence

>retro_etel_1220
ACTGTTACAATTTTCTTTGAAAACAAGTGGCAAATTGAAAGACAAATTATTTGGGGGGATGTCCAGCTACCAGCAGACTA
CACTAAAGACATCACGGAATGGGATGAGGTAGAGGTTTATTCTCGAGCCAAGGGACAGGAACTTTGTGGCTGGTGGCTGG
CTTGGACACAGCTGATAAAAGGAGATTTCTATGTCATTGAATATGCTGGCAGCAGTGCTACTTACTATGAAATTGTCACC
CTGGAGCGACCTTGGCCAGTCAATCCCAACCCCCTTGCAACCAAAGGCAGCTTCTTCAAGGTCACCATGGCTGTTCCTGA
GGATCTCAGAGAGGCCTGCTTCAAGGAAAACATCCATAAGAGTTCAAAACAGATTTGAGAGCTAGCTGCATCTTTCTCAA
CTTCACAAATAGCAAGCTGTTTATTCTGCCAATCCCTTTGAAGTGGGAATCTCTGTTGGGGAACTTGAATTTTTGAGAAC
TAAGCACCAAATTGCTACTTATGTCTCCTAATGAAGAAGTTACCAAACACCTAGAGACAAGTAAGAAATTGGCAGCAGCA
TCCTAGGAGGAGTTCACAGTGCGAGAGGATCTGATGGGACTGGAAATTGGGACTTACACTGCTAACATCCAGGAGGTCTG
AAAATTACCTGGGGTGACCACCATTGAGATGGATGAAGAGACCTGTGGTTTCCACCTCTATGGGAAGATTCTTGAGGCAT
GCCGGCAGGCCTGAAGTTACCTTGAGTTTTCTGAGAACTTGGTGCCAGTACCCAGGAATCTTGTTGTCAAAGGCACTGGA
AGGAACGGGAAAGTGATCCAGGAGATTGTGGACAAATCTGCTGTGGTGAGGGTCTGAGTGCAAGGAGAAAATGACAAGAA
GAAACCAAGGGAGGAGGGAATGATTCCCTGCATATTTGTTGGCACCCGAGGGAATATCAGCAATTCTCAGTCTCTGCTGG
AATGTCACCTTTCCTACCTGCAGTAGCTGGAGCAGCTCTGTTTGGAGAGGCTGCAA

Alignment

ORF - retro_etel_1220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYSRANEQEPCGWWLARVRMMKGDFYVIEY
          .VTIFFEN.WQ.ERQI..GDV.LP..ADY.K.ITE.DEVEVYSRA..QE.CGWWLA.....KGDFYVIEY
Retrocopy TVTIFFENKWQIERQIIWGDVQLP--ADYTKDITEWDEVEVYSRAKGQELCGWWLAWTQLIKGDFYVIEY

Parental  AACDATYNEIVTLERLRPVNPSPLATKGSFFKVTMAVPEDLREACSNENVHK-EFKKALGANCIFLNITN
          A...ATY.EIVTLER..PVNP.PLATKGSFFKVTMAVPEDLREAC..EN.HK.EFK..L.A.CIFLN.TN
Retrocopy AGSSATYYEIVTLERPWPVNPNPLATKGSFFKVTMAVPEDLREACFKENIHK<EFKTDLRASCIFLNFTN

Parental  SELFILSTTEAPVKRASLL-DMHFRSLRTKLLLMSRNEEATKHLETSKQLAAAFQEEFTVREDLMGLAIG
          S.LFIL.....P.K..SLL....F..L.TKLLLMS.NEE.TKHLETSK.LAAA..EEFTVREDLMGL.IG
Retrocopy SKLFILPI---PLKWESLLGNLNF*ELSTKLLLMSPNEEVTKHLETSKKLAAAS*EEFTVREDLMGLEIG

Parental  THGANIQQARKVPGVTAIELGEETCTFRIYGETPEACRQARSYLEFSEDSVQVPRNLVGKVIGKNGKVIQ
          T..ANIQ...K.PGVT.IE..EETC.F..YG...EACRQA.SYLEFSE..V.VPRNLV.K..G.NGKVIQ
Retrocopy TYTANIQEV*KLPGVTTIEMDEETCGFHLYGKILEACRQA*SYLEFSENLVPVPRNLVVKGTGRNGKVIQ

Parental  EIVDKSGVVRVRVEGDNDKRNPREEGMVPFIFVGTRENISNAQALLEYHLSYLQEVEQLRLERLQ
          EIVDKS.VVRV.V.G.NDK..PREEGM.P.IFVGTR.NISN.Q.LLE.HLSYLQ..EQL.LERLQ
Retrocopy EIVDKSAVVRV*VQGENDKKKPREEGMIPCIFVGTRGNISNSQSLLECHLSYLQ*LEQLCLERLQ

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_1220 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000018613	1 retrocopy	retro_etel_1220 ,
Monodelphis domestica	ENSMODG00000007179	1 retrocopy	retro_mdom_2009,
Rattus norvegicus	ENSRNOG00000011876	1 retrocopy	retro_rnor_371,
Sarcophilus harrisii	ENSSHAG00000015678	1 retrocopy	retro_shar_400,