RetrogeneDB ID: retro_shar_585

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850527.1:113701..114445(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000004630
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF2B
• Ensembl ID: ENSSHAG00000005314
• Aliases: None
• Description: general transcription factor IIB [Source:HGNC Symbol;Acc:4648]

Sequence

>retro_shar_585
GAGACTCAGAATCCTCTCCTGTGTGATGGAGACTTCACAACATTAATTGGCAAGGGTACTGGAGCAGCAAGCTTTGATGA
ATTTGGAAATTCAAAGTATCAAAATCACAGAACAATGAGCAGTTCTGATCGTGCAATGATGAATGCTTTCAAAGAAATTA
CTACTATGGCAGACAGAATCAACCTCCCTCGAAATATGGTTGATCGAACAAATTATTTATTCAAGCAAGTATATGAACAG
AAGAGGCTGAAGGGAAGAGCTAATGATGCCATAGCTTCTGCTTGTCTCTATATTGCCTGTAGACAAGAGGGTGTTCCTAA
AACATTTAAAGAAATATGTGCAGTTTCACAGATTTCCAAGAAAGAAATAGGCCAGTGTTTTAAGCTAATTTTGAAGGCTT
TAGAAACCAGTGTGGATTTGATCACAGCAGGGGATTTCACGTCAAGGTTTTGTTCCAACCTTGGTCTCCCTAAACAAATA
CAGATGGCAGCTGCACATACTGCCCGGAAAACTGTGGAGCTGGACTTGGTGCCCAGCAGAAGTCCCATTTCTGTGGCTGC
TGCAGCGATTTATATGGCTTCCCAAGCTTCTGCAGAGAAAAGGACTCAGAAAGAAATTGGAGACATTGCTGGAGTTGCTG
ATGTTACAATCCGGCAGTCTTACACACTCCTCTATCCTCAAGCCCCAGATCTGTTTCCTGCAGACTTCAAATTCAACACC
CCTGTGGACAAACTACCCCAATTG

Alignment

ORF - retro_shar_585 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 78.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSQNPLLSDGDLTTMIGKGTGAASFDEFGNSKYQNHRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRT
          ..QNPLL.DGD.TT.IGKGTGAASFDEFGNSKYQNHRTMSSSDRAMMNAFKEITTMADRINLPRN.VDRT
Retrocopy ETQNPLLCDGDFTTLIGKGTGAASFDEFGNSKYQNHRTMSSSDRAMMNAFKEITTMADRINLPRNMVDRT

Parental  NNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDL
          N.LFKQVYEQK.LKGRANDAIASACLYIACRQEGVP.TFKEICAVS.ISKKEIG.CFKLILKALETSVDL
Retrocopy NYLFKQVYEQKRLKGRANDAIASACLYIACRQEGVPKTFKEICAVSQISKKEIGQCFKLILKALETSVDL

Parental  ITTGDFMSRFCSNLGLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIA
          IT.GDF.SRFCSNLGLPKQ.QMAA.H.ARK.VELDLVP.RSPISVAAAAIYMASQASAEKRTQKEIGDIA
Retrocopy ITAGDFTSRFCSNLGLPKQIQMAAAHTARKTVELDLVPSRSPISVAAAAIYMASQASAEKRTQKEIGDIA

Parental  GVADVTIRQSYRLIYPRAPDLFPADFKFDTPVDKLPQL
          GVADVTIRQSY.L.YP.APDLFPADFKF.TPVDKLPQL
Retrocopy GVADVTIRQSYTLLYPQAPDLFPADFKFNTPVDKLPQL

Legend:

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_585 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028271	1 retrocopy	retro_mmus_3165,
Sarcophilus harrisii	ENSSHAG00000005314	1 retrocopy	retro_shar_585 ,
Tupaia belangeri	ENSTBEG00000001398	2 retrocopies	retro_tbel_1988, retro_tbel_2988,
Tursiops truncatus	ENSTTRG00000011903	1 retrocopy	retro_ttru_1823,