RetrogeneDB ID: retro_etel_1927

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_314947:29002..29479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSETEG00000015340
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_etel_1927
GCGGTGGAGGAGCCGCAGCTGCTGCACCGGGCCGGGATCTGTAAGTGGTTCAACATGCGCATGGGGTTCGGCTTCCTGTC
CATGACCGCCCGTGCCAGGGTCGCGCTTGACCCCCCGGTGGACGTCTTTGTGCACCAGAGTAAGCTGCACATGGAGGGCT
TCCGGAGCCTAAAAGAGGGAGAAGCTGTGGAGTTCACCTTTAAGAAGTCTGCTAAGGGCCTGGAGTCCATCCGAGTCATC
GGACCTGGTGGGGTGTTCTGTATCGGGAGTGAGAGGAGACCCAAGGGGAAGAACATGCAGAAGCGCAGGTCAAAGGGAGA
CAGATGCTTCCACTGTGGAGGTCTAGACCATCATGCCAAGGAATGCAAACTGCCACCCCAGCCTAAGAAGTGTCACTTCT
GCCAAAGCATCAGCCATATGGTAGCCTCTTGTCCAGTGAAAGGGCCAGCAGGCCCCCAGCTCACAGGGAAAGCCCGC

Alignment

ORF - retro_etel_1927 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEEESHVLHGTGHCKWFNVRMGFGFISMISREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKS
          A.EE...LH..G.CKWFN.RMGFGF.SM..R....LD.PVDVFVHQSKL.MEGFRSLKEGE.VEFTFKKS
Retrocopy AVEEPQLLHRAGICKWFNMRMGFGFLSMTARARVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKS

Parental  CKGLESIRVTGPGGSPCVGSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQPKKCHYCQSITHM
          .KGLESIRV.GPGG..C.GSERRPKGK..QKR..KGDRC..CGGLDHHAKEC.LPPQPKKCH.CQSI.HM
Retrocopy AKGLESIRVIGPGGVFCIGSERRPKGKNMQKRRSKGDRCFHCGGLDHHAKECKLPPQPKKCHFCQSISHM

Parental  VANCPHKTVAQPPTSSQGR
          VA.CP.K..A.P......R
Retrocopy VASCPVKGPAGPQLTGKAR

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_1927 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927 ,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815,