RetrogeneDB ID: retro_etel_1033

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_202553:8824..9520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000014331
• Aliases: None
• Description: None

Sequence

>retro_etel_1033
TCCTACCTGGGCGGCATGGTGTCCAGCAACTCAGCACTATAGTGTGTCAACTACCTCACTCAGGTTCTGGGTAAATCCTG
CAAGCCAATTCCAGCCATGCTCCTTAGGGTGACTCTCCTGAAGAAGAACCCGCTGCCCAATACCTGTGTGTGTGTGTTGT
TAATTGTAGCTTCAGTAGCTGTTTTCCTGTACAAGCCAAAGGAAGGTTGTTGGAAGAACACACAATTGCCTAAATTGCCT
ATGGAGAGCCACTCCTGCTCTTGTCTCTAACCCTGGATGGACTGACAGACGTTTTCCAGGACCACATGCAAGCTCATTAT
CAAACATGCCCCAATCACGTGATGTTGAACATCAACCTTGTGGTCCACCATGCTGCTGGGCGCCGGGATGCTGTTCACTG
GGAAGCTCTGGGAGTCCCTGTGCTTTGCAGAGAGGTACCCTGCCACCATCTCTAACATCCTGCTCTTTGGCCTGACCAGT
GCCCTGGGTCAGAGCTGCATCTTTAGGATCATTGTACTTTGGGGCCCCTGACCTGCTCAAACATCCCCGCAGTTCACAAG
TTCTTCCCCATCTTGGTCTCTGTGATCCTCTTTGCCAACCCTGTCAGCTCCATGCAGAGGGTCGGCACTGTGCTGGGGTT
CCTGGATCTCCGTCTCGTAAAAAAACGTTGGGAAAGGAGCCAAAAAGACTTTTCAC

Alignment

ORF - retro_etel_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.4 %
• Parental protein coverage: 80.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SYLGAMVSSNSALQFVNYPTQXXXXXXXXXXXMLLGVTLLKKKYPL-AKYLCVLLIVAGVALFMYKPKKV
          SYLG.MVSSNSAL..VNY.TQ...........MLL.VTLLK.K.PL.A.YLCV...............K.
Retrocopy SYLGGMVSSNSAL*CVNYLTQVLGKSCKPIPAMLLRVTLLK-KNPL<AQYLCVCVVNCSFSSCFPVQAKG

Parental  VGVEEHT---IGYGELLLLLSLTLDGLTGVSQDHMRAHYQTGSNHMMLNINL-WSTLMLGAGILFTGELW
          ...EEHT...I.YGE.LLLLSLTLDGLT.V.QDHM.AHYQT..NH.MLNINL.WST..LGAG.LFTG.LW
Retrocopy RLLEEHTIA*IAYGEPLLLLSLTLDGLTDVFQDHMQAHYQTCPNHVMLNINL>WSTMLLGAGMLFTGKLW

Parental  EFLSFAERYPAIISNILLFGLTSALGQSFIFMTVVYF-GPLTCSIITTTRKFFTILASVILFANPISSMQ
          E.L.FAERYPA.ISNILLFGLTSALGQS.IF...V...GPLTCS.I....KFF.IL.SVILFANP.SSMQ
Retrocopy ESLCFAERYPATISNILLFGLTSALGQSCIFRIIVLW<GPLTCSNIPAVHKFFPILVSVILFANPVSSMQ

Parental  WVGTVLVFLGLGLDAK-FGKGAKKTSH
          .VGTVL.FL.L.L..K..GKGAKKT.H
Retrocopy RVGTVLGFLDLRLVKK>VGKGAKKTFH

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_1033 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009256	2 retrocopies	retro_dnov_1341, retro_dnov_2192,
Echinops telfairi	ENSETEG00000014331	2 retrocopies	retro_etel_1033 , retro_etel_1819,