RetrogeneDB ID: retro_etel_1525

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_276961:47118..47859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAP1
• Ensembl ID: ENSETEG00000001865
• Aliases: None
• Description: small ArfGAP 1 [Source:HGNC Symbol;Acc:19651]

Sequence

>retro_etel_1525
AAGAAAGGGAAAAAAAAAAAAAAAAAGGAGCCAGAGAGTCTTCCAAAACCTCTTACAACTGGAAAGCTGCAGAAGAAGGA
AGATCAGCAATTGGAACTTCAAAAAAGTACTAGCCTTAAGAAAACCACAGAGCCACTGTGGATCTTTTAGGACCTGATGG
CCCTGCTGAAGCACCAGTAACCAATGGGAACACAACCACGATGCCAGCCCTGAGTGATGACCCGGACATCTTTGGACCAA
TGATCTCGAATCCCTTGCCTCCAGGTCAGGGGACGTCCACTGGACCAGTAGCTGCCCCCGTGTCTACAGTAACATCTGGT
GATCTGGATCTATTCACTGAACAAACCACAAAATCCGAAGAATCCACAAAGAAACAGCTCTCCAAAGATTCCATCTTATC
TCTGTATGGTACCGGGACCATTCAGCAGCAGACTACGCCTGGTGTGTTTATGGGGCCCACAAATATACCATTTACCTCAC
AAGCACCAACTGTATTTCAAGGTTTTCCAGCAATGGGAGTTCCTGTGTCTGCAGCTCCTGGCCTTATGGGAAATGTAATG
GGACAGAGCACAAATATGATGGTGGGCGTGCCCATACCTATTGGGTTTATGGGGAATGCACAAACTGGTGTGATGCCACT
TCCTCAAAATGTTGGCGGAATGGCTGCGTCCCAGAGTAAGTTCGGTGTGCCGCAAGCTCAGCAGCCCCAGTGGAGTCTCT
CACAGACGAACCAGCAAATGG

Alignment

ORF - retro_etel_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.72 %
• Parental protein coverage: 53.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKEEKKKEKEPEKPSKPLTTEKLQKKEDQQLELKKSTSPKKTTEP-TVDLLGLDGPAEAPVTNGNPTTMP
          KK.......EPE...KPLTT.KLQKKEDQQLEL.KSTS.KKTTEP.TVDLLG.DGPAEAPVTNGN.TTMP
Retrocopy KKGXXXXXXEPESLPKPLTTGKLQKKEDQQLELQKSTSLKKTTEP<TVDLLGPDGPAEAPVTNGNTTTMP

Parental  ALSDDLDIFGPMISNPLPPGQGTSTGPVAAPVSTVTSGDLDLFTEQTTKSEESTKKQLSKDSILSLYGTG
          ALSDD.DIFGPMISNPLPPGQGTSTGPVAAPVSTVTSGDLDLFTEQTTKSEESTKKQLSKDSILSLYGTG
Retrocopy ALSDDPDIFGPMISNPLPPGQGTSTGPVAAPVSTVTSGDLDLFTEQTTKSEESTKKQLSKDSILSLYGTG

Parental  TIQQQTTPGVFMRPTNMPFTSQAPTAFQGFPAMGVPVPAAPGLMGNVMGQSPNMMVGVPIPNGFMGNAQT
          TIQQQTTPGVFM.PTN.PFTSQAPT.FQGFPAMGVPV.AAPGLMGNVMGQS.NMMVGVPIP.GFMGNAQT
Retrocopy TIQQQTTPGVFMGPTNIPFTSQAPTVFQGFPAMGVPVSAAPGLMGNVMGQSTNMMVGVPIPIGFMGNAQT

Parental  AVMPLPQNVVGPQGGM-VGPMAAASQSKFGVPQAQQPQW
          .VMPLPQNV.G......V........S..GV.......W
Retrocopy GVMPLPQNVGGMAASQ>VSSVCRKLSSPSGVSHRRTSKW

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_1525 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	ENSETEG00000001865	1 retrocopy	retro_etel_1525 ,
Felis catus	ENSFCAG00000007247	1 retrocopy	retro_fcat_1157,
Loxodonta africana	ENSLAFG00000007948	1 retrocopy	retro_lafr_530,
Mus musculus	ENSMUSG00000026155	1 retrocopy	retro_mmus_3253,