RetrogeneDB ID: retro_tbel_1988

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6135:339024..339630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2B
• Ensembl ID: ENSTBEG00000001398
• Aliases: None
• Description: general transcription factor IIB [Source:HGNC Symbol;Acc:4648]

Sequence

>retro_tbel_1988
ACAATGAGTAGTTCTGATCAGGCAATAATGAATGCATTCAAGGAAATCACTATCATGGCAGACAGACTCAATCTCCCTCG
AAATATAATTCATCAAACAAATAATTTATTCAAGCAAGTATATGAATAGAAGAGCCTGAAGGAAGAGCTAATGATGCCAT
AGCTTCTGCTTGTCTCTATATCGCCTGTAGATAAGAAGGGGTTCCTAGGACATTTAAAGAAATATGTGCTGTATCACGAG
TTTAAAGAAAGAAATTGGTCGATATTTTGAACTTATTTTGAAAGCTTTAGAAACCAGTGTGGATTTGATTACAGTGGGGG
ACTTCATGTACAGGTTCTGTTCCAAACTTTGTTTTCCTAAACAAGTTCAGATGGCAGCTACACATGTTGTCCGCAAAGCT
GTGGAGCTGGACTTGGTTTCTGGAAGGAACCCCATCTGTGCGGCAGCAGCAGCTATTTACATGGCCTCTCAGGCATCAGC
TGAGAAGAGGACCCAAAAAGAAATTGAGATATTGCTGGTGTTGCTGATGTTACAATCAGACAGTACTACAGACTGATCTA
TCCTCAAACTCCAGGTCTGTTTCCCACAGACTTCAAATTTGACACC

Alignment

ORF - retro_tbel_1988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 65.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TMSSSDRAMMNAFKEITTMADRINLPRNIIDRTNNLFKQVYEQKSLK-GRANDAIASACLYIACRQEGVP
          TMSSSD.A.MNAFKEIT.MADR.NLPRNII..TNNLFKQVYE.KSLK.GRANDAIASACLYIACR.EGVP
Retrocopy TMSSSDQAIMNAFKEITIMADRLNLPRNIIHQTNNLFKQVYE*KSLK<GRANDAIASACLYIACR*EGVP

Parental  RTFKEICAVSRI-SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELD
          RTFKEICAVSR...KKEIGR.F.LILKALETSVDLIT.GDFM.RFCS.LC.PKQVQMAATH..RKAVELD
Retrocopy RTFKEICAVSRV<LKKEIGRYFELILKALETSVDLITVGDFMYRFCSKLCFPKQVQMAATHVVRKAVELD

Parental  LVPGRSPISVAAAAIYMASQASAEKRTQKEIG-DIAGVADVTIRQSYRLIYPRAPDL-PTDFKFDT
          LV.GR.PI..AAAAIYMASQASAEKRTQKEI..DIAGVADVTIRQ.YRLIYP..P.L.PTDFKFDT
Retrocopy LVSGRNPICAAAAAIYMASQASAEKRTQKEIE<DIAGVADVTIRQYYRLIYPQTPGLFPTDFKFDT

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1988 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1988 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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,