RetrogeneDB - Retrocopy retro_etel

                        
>retro_etel_2174
GAGCCGCTGCTGCTGGCAGAACTCAAGCCCAGGCGCCCCCCACCAGTTTGATTGGAAGTCTCAGCTGTGAGACCTGGAGT

GTCGTCTTTCTCTCTCGACGGTTCCTGGTCTGCCTGGTCTCAAGGACACTGTATTGTCAAGCTGATCCCCTGGCCGCTGG

AGGAAGAGTTCATCCCCAAAGGGTTTGAAGCCAAGAGCTGAAGCAGCAAAAATGATCCCAAAGGACTAGGCAGCCCCAAA

GAGAAGACCCTGGACAGCGGTCAGATTGTCCGGGGCTTGGCTTTCAGCCCGTGGCCCTCCCCACCCAGCAGGTGTCTCTG

GGCATGCCACCATCCCCAAGTGCCAGATGTCTCATGCCTGATCCTGGCCACAGGGCTCAACGTTGGGCAGATCAAGATTT

GGGAGGTGCAGACAGGGTTCCTGCTTTTGAATCTTTCGGGCCACCAGGATGTCATGAGAGATCTGAGCTTCACACCCAGT

GTTAGTTTGATCCTGGTCTCTGTATCCCGGGACCAAACTCTTCGCATCTGGGCCCTGAATAAACATGGTAAACAGCTCCA

GGTGTTATCAGGCCACCTGCAATGGGTTTACTGCTGCTCCATCTCCCCGGACTGCAGCATGCTGTGCTCTGCAGCTGGAG

AGAAGTCTGTCTTTCTATGGAGCATGCACACTAATCCGGAGCTGGAGGGCCACCAGCGCAGTGTCCTCTCTTGTGATTTC

TTCCCTGACTCAGCCTTGCTTGTCACGGCTTCCTACGGACACCAACGTGATCACGTGAGACCCCTACACTGGCGAGGGGC

TGCGGTCACTCCACCACACCCAGCTCGACCCCCCATGGACGACAGTGATGTGCACATCAGCTCGCTGAGGTCCGTGTGCT

TCTCTCCACAAGGCCTGGACCTGGGCCACAGTGGTGCATGACAGGCTCTTCAGCATCTGGGCGCTGGAACTGAAAGCTCC

CTTCCCGCTTGCTCCCATGACCAGTGATCTGTGTGGCACCTTCTTC

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:

                                ParentalEPLLLAELKP-GRPHQFDWKS-SCETWSV-AFSPDGSWFAWSQGHCIVKLIPWPLEEQFIPKGFEAKSRS
EPLLLAELKP.G.PHQFDWKS.SCETWSV..FS.DGSW.AWSQGHCIVKLIPWPLEE.FIPKGFEAKS.S
RetrocopyEPLLLAELKP>GAPHQFDWKS>SCETWSV>SFSLDGSWSAWSQGHCIVKLIPWPLEEEFIPKGFEAKS*S
ParentalSKNDPKGRGSPKEKTLDCGQIVWGLAFSPWPSPPSRRLWARHHPQVPDVSGLILATGLNDGQIKIWEVQT
SKNDPKG.GSPKEKTLD.GQIV.GLAFSPWPSPPSR.LWA.HHPQVPDVS.LILATGLN.GQIKIWEVQT
RetrocopySKNDPKGLGSPKEKTLDSGQIVRGLAFSPWPSPPSRCLWACHHPQVPDVSCLILATGLNVGQIKIWEVQT
ParentalGFLLLSLSGHQDVVRDLSFTPSGSLILVSASRDKTLRIWDLNKHGKQIQVLSGHLQWVYCCSISPDCSML
GFLLL.LSGHQDV.RDLSFTPS.SLILVS.SRD.TLRIW.LNKHGKQ.QVLSGHLQWVYCCSISPDCSML
RetrocopyGFLLLNLSGHQDVMRDLSFTPSVSLILVSVSRDQTLRIWALNKHGKQLQVLSGHLQWVYCCSISPDCSML
ParentalCSAAGEKSVFLWSMRSYTLIRKLEGHQSSVVSCDFSPDSALLVTASY-DTNVIMWDPYTGERLRSLHHTQ
CSAAGEKSVFLWSM........LEGHQ.SV.SCDF.PDSALLVTASY.DTNVI..DPYTGE.LRSLHHTQ
RetrocopyCSAAGEKSVFLWSMHTNP---ELEGHQRSVLSCDFFPDSALLVTASY>DTNVIT*DPYTGEGLRSLHHTQ
ParentalLD-PPMDDSDVHISSLRSVCFSPEGLYL-ATVADDRLLRIWALELKAPVAFAPMTNGLCCTFF
LD.PPMDDSDVHISSLRSVCFSP.GL.L.ATV..DRL..IWALELKAP...APMT..LC.TFF
RetrocopyLD<PPMDDSDVHISSLRSVCFSPQGLDL>ATVVHDRLFSIWALELKAPFPLAPMTSDLCGTFF

                            

                            Legend:
                            
                                *Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

                        

RNA-Seq - click to see more details

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Echinops telfairi was not studied using ChIP-Seq data.

EST - click to see more details

Echinops telfairi was not studied using EST data.

TSS - click to see more details

Echinops telfairi was not studied using FANTOM5 data.

Lab - click to see more details

retro_etel_2174 was not experimentally validated.

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.

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,

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

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

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_etel_2174