RetrogeneDB ID: retro_etel_1984

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321803:3594..4174(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000010897
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNB1
• Ensembl ID: ENSETEG00000020012
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), beta polypeptide 1 [Source:HGNC Symbol;Acc:4396]

Sequence

>retro_etel_1984
TCCTGCTGCCGCTTCCTAGATGACAATCAGATCGTCACCAGCTGTGGAGACACCACCTGTGCGCTGTGGGATATAGAGAC
TGGCCAGCAGACAGCCACGTTCACAGGAACACCAGGGACGTCATGAGCCTCTCCCTGGCTCCAGACACTAGATTGTTTGT
TTCTGGTGCTTGTGACGCTTCGGCCATGCTCTGGGACGTGCGAGAAGGGATGTGTCGACAGACCTTTCACTGCCCACGAG
TCAGACATCAGCGCCGATCTGTTTCTTTTCCAAATGGCAATGCATTTGCCAACGGGCTCAAGAATGCCACCTGGCAGGCT
GTTTGACCTCCGCGCAGACCAAGAAGCTCATGACCGTACTCCCACGAGGACAGCATCTGTGGGATCACCTGTCTGCTTCT
CCAAGAGCGGCCGCCGCCTCCTTGCTGGCTATGACGACTCAACTGCAGTGTCTGGGATGCGCTCAAGGCCCAGAGGGCTG
GTGTCCTGGCTGGGCATGACCACCGTGTCAGCTGCGTGGGGTGACTGATGATGGCATGGCTGTGGCGACGGGGTCCTGGG
ACAGCTTCCTCAAGATCTGG

Alignment

ORF - retro_etel_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  SCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG-HTGDVMSLSLAPDTRLFVSGACDASAKLWDVRE
          SCCRFLDDNQIVTS.GDTTCALWDIETGQQT.TFTG..T.DVMSLSLAPDTRLFVSGACDASA.LWDVRE
Retrocopy SCCRFLDDNQIVTSCGDTTCALWDIETGQQTATFTG<NTRDVMSLSLAPDTRLFVSGACDASAMLWDVRE

Parental  GMCRQT-FTGHESDINA-ICF-FPNGNAFATGSDDATC-RLFDLRADQE-LMT-YSHDNIICGITSVSFS
          GMCRQT.FT.HESDI.A.ICF.FPNGNAFA.G...AT..RLFDLRADQE.LMT.YSH...ICGIT.....
Retrocopy GMCRQT>FTAHESDISA>ICF>FPNGNAFANGLKNATW>RLFDLRADQE>LMT>YSHEDSICGITCLLLQ

Parental  K-SGRLLLAGYDD-FNCNVWDALKADRAGVLAGHDNRVSCL-GVTDDGMAVATGSWDSFLKIW
          ....RLL.AGYDD..NC.VWDALKA.RAGVLAGHD.RVSC..GVTDDGMAVATGSWDSFLKIW
Retrocopy E>GRRLL-AGYDD<LNCSVWDALKAQRAGVLAGHDHRVSCV<GVTDDGMAVATGSWDSFLKIW

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_1984 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019216	1 retrocopy	retro_cfam_1083,
Echinops telfairi	ENSETEG00000020012	1 retrocopy	retro_etel_1984 ,
Rattus norvegicus	ENSRNOG00000016638	1 retrocopy	retro_rnor_1660,