RetrogeneDB ID: retro_etel_1866

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_309276:46923..47335(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPC2
• Ensembl ID: ENSETEG00000003719
• Aliases: None
• Description: Niemann-Pick disease, type C2 [Source:HGNC Symbol;Acc:14537]

Sequence

>retro_etel_1866
TTGCGTGCCCTCGCCACCGCGATCCTGCTGCTGGCGCTCAACGCCGGGGTCGATAGCCGAGCCGGTGAGGTTCCGGGACT
GTGGGTCTATGGTGGGAACTGTACAGGAGGTGAATGTAAGCCCATGCCCCAACCAGACATGCCAGCTGACCAAAGGACAG
TCTTACAGTGTGGAAGTCACCTTCACCAGCGAGACCAACTCCCATAACAGCACAGCCGTGGTGCATGGCATTGTGCTGGG
CGTCCCCTTCCCCTTTGCCATGCCTGTGTCCGACGGCTGCAAGAGTGGCATCATCTGCCCCATCCAAAAAGGAAAGAGCT
ATAACTACCTGAATAAACTCCCGGTGAAGAGTGAATACCCCTCCGTAAAGCTGGTGGTGAAGTGGGAACTTGTGGATGAC
AAGAAGCAGTCT

Alignment

ORF - retro_etel_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.43 %
• Parental protein coverage: 95.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRALATAILLLALNSA-SIAEPVGFRDCGSVVGTVQEVNVSPCPNQPCQLIKGQSYSVNVTFTSKTSSNN
          .RALATAILLLALN...SIAEPV.FRDCGS.VGTVQEVNVSPCPNQ.CQL.KGQSYSV.VTFTS.T.S.N
Retrocopy LRALATAILLLALNAG>SIAEPVRFRDCGSMVGTVQEVNVSPCPNQTCQLTKGQSYSVEVTFTSETNSHN

Parental  STAVVHGIVLGVPLPFAIPVSDGCKSGISCPIQKGKCYNYLNKLPVKSEYPSXXL-VKGRLLDGNQET
          STAVVHGIVLGVP.PFA.PVSDGCKSGI.CPIQKGK.YNYLNKLPVKSEYPS..L.VK..L.D.....
Retrocopy STAVVHGIVLGVPFPFAMPVSDGCKSGIICPIQKGKSYNYLNKLPVKSEYPSVKLVVKWELVDDKKQS

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_1866 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016932	1 retrocopy	retro_cfam_2050,
Choloepus hoffmanni	ENSCHOG00000009488	1 retrocopy	retro_chof_2335,
Echinops telfairi	ENSETEG00000003719	2 retrocopies	retro_etel_1610, retro_etel_1866 ,
Loxodonta africana	ENSLAFG00000002876	1 retrocopy	retro_lafr_289,
Tursiops truncatus	ENSTTRG00000013025	1 retrocopy	retro_ttru_85,