RetrogeneDB ID: retro_etel_2174

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_87712:1..1007(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000001185
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WSB2
• Ensembl ID: ENSETEG00000018534
• Aliases: None
• Description: WD repeat and SOCS box containing 2 [Source:HGNC Symbol;Acc:19222]

Sequence

>retro_etel_2174
GAGCCGCTGCTGCTGGCAGAACTCAAGCCCAGGCGCCCCCCACCAGTTTGATTGGAAGTCTCAGCTGTGAGACCTGGAGT
GTCGTCTTTCTCTCTCGACGGTTCCTGGTCTGCCTGGTCTCAAGGACACTGTATTGTCAAGCTGATCCCCTGGCCGCTGG
AGGAAGAGTTCATCCCCAAAGGGTTTGAAGCCAAGAGCTGAAGCAGCAAAAATGATCCCAAAGGACTAGGCAGCCCCAAA
GAGAAGACCCTGGACAGCGGTCAGATTGTCCGGGGCTTGGCTTTCAGCCCGTGGCCCTCCCCACCCAGCAGGTGTCTCTG
GGCATGCCACCATCCCCAAGTGCCAGATGTCTCATGCCTGATCCTGGCCACAGGGCTCAACGTTGGGCAGATCAAGATTT
GGGAGGTGCAGACAGGGTTCCTGCTTTTGAATCTTTCGGGCCACCAGGATGTCATGAGAGATCTGAGCTTCACACCCAGT
GTTAGTTTGATCCTGGTCTCTGTATCCCGGGACCAAACTCTTCGCATCTGGGCCCTGAATAAACATGGTAAACAGCTCCA
GGTGTTATCAGGCCACCTGCAATGGGTTTACTGCTGCTCCATCTCCCCGGACTGCAGCATGCTGTGCTCTGCAGCTGGAG
AGAAGTCTGTCTTTCTATGGAGCATGCACACTAATCCGGAGCTGGAGGGCCACCAGCGCAGTGTCCTCTCTTGTGATTTC
TTCCCTGACTCAGCCTTGCTTGTCACGGCTTCCTACGGACACCAACGTGATCACGTGAGACCCCTACACTGGCGAGGGGC
TGCGGTCACTCCACCACACCCAGCTCGACCCCCCATGGACGACAGTGATGTGCACATCAGCTCGCTGAGGTCCGTGTGCT
TCTCTCCACAAGGCCTGGACCTGGGCCACAGTGGTGCATGACAGGCTCTTCAGCATCTGGGCGCTGGAACTGAAAGCTCC
CTTCCCGCTTGCTCCCATGACCAGTGATCTGTGTGGCACCTTCTTC

Alignment

ORF - retro_etel_2174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.84 %
• Parental protein coverage: 84.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EPLLLAELKP-GRPHQFDWKS-SCETWSV-AFSPDGSWFAWSQGHCIVKLIPWPLEEQFIPKGFEAKSRS
          EPLLLAELKP.G.PHQFDWKS.SCETWSV..FS.DGSW.AWSQGHCIVKLIPWPLEE.FIPKGFEAKS.S
Retrocopy EPLLLAELKP>GAPHQFDWKS>SCETWSV>SFSLDGSWSAWSQGHCIVKLIPWPLEEEFIPKGFEAKS*S

Parental  SKNDPKGRGSPKEKTLDCGQIVWGLAFSPWPSPPSRRLWARHHPQVPDVSGLILATGLNDGQIKIWEVQT
          SKNDPKG.GSPKEKTLD.GQIV.GLAFSPWPSPPSR.LWA.HHPQVPDVS.LILATGLN.GQIKIWEVQT
Retrocopy SKNDPKGLGSPKEKTLDSGQIVRGLAFSPWPSPPSRCLWACHHPQVPDVSCLILATGLNVGQIKIWEVQT

Parental  GFLLLSLSGHQDVVRDLSFTPSGSLILVSASRDKTLRIWDLNKHGKQIQVLSGHLQWVYCCSISPDCSML
          GFLLL.LSGHQDV.RDLSFTPS.SLILVS.SRD.TLRIW.LNKHGKQ.QVLSGHLQWVYCCSISPDCSML
Retrocopy GFLLLNLSGHQDVMRDLSFTPSVSLILVSVSRDQTLRIWALNKHGKQLQVLSGHLQWVYCCSISPDCSML

Parental  CSAAGEKSVFLWSMRSYTLIRKLEGHQSSVVSCDFSPDSALLVTASY-DTNVIMWDPYTGERLRSLHHTQ
          CSAAGEKSVFLWSM........LEGHQ.SV.SCDF.PDSALLVTASY.DTNVI..DPYTGE.LRSLHHTQ
Retrocopy CSAAGEKSVFLWSMHTNP---ELEGHQRSVLSCDFFPDSALLVTASY>DTNVIT*DPYTGEGLRSLHHTQ

Parental  LD-PPMDDSDVHISSLRSVCFSPEGLYL-ATVADDRLLRIWALELKAPVAFAPMTNGLCCTFF
          LD.PPMDDSDVHISSLRSVCFSP.GL.L.ATV..DRL..IWALELKAP...APMT..LC.TFF
Retrocopy LD<PPMDDSDVHISSLRSVCFSPQGLDL>ATVVHDRLFSIWALELKAPFPLAPMTSDLCGTFF

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_2174 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003651	1 retrocopy	retro_chof_870,
Echinops telfairi	ENSETEG00000004321	1 retrocopy	retro_etel_1046,
Echinops telfairi	ENSETEG00000018534	2 retrocopies	retro_etel_1750, retro_etel_2174 ,
Microcebus murinus	ENSMICG00000005913	1 retrocopy	retro_mmur_1573,
Myotis lucifugus	ENSMLUG00000002114	1 retrocopy	retro_mluc_2097,
Macaca mulatta	ENSMMUG00000010236	1 retrocopy	retro_mmul_1466,
Mus musculus	ENSMUSG00000029364	1 retrocopy	retro_mmus_810,