RetrogeneDB ID: retro_tbel_2435

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110621:82470..82823(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSU72
• Ensembl ID: ENSTBEG00000010136
• Aliases: None
• Description: SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]

Sequence

>retro_tbel_2435
TCCACGCTGCGGGTGGCCGTGGTGTGCTCCAACAACCAGAACCGGAGCATGTAGGCGCACAACCTCCTCAGCAAGCGAGG
GTTCTGCGTCCGCTCCTTTGGCACCGGGACGAGAGTGAAGCTCCCGGGCCCGGCCCCGACAAGCCCAATGTCTACGACTT
CCACACCACCTACGACCAGATGTACAAGGACCTGCTGCACAAGGACGAGAAGTTGTACACGCGCAACGGCGTCTTACACA
TGCTGGGCAGAAACAAGAGGATCAAGCCCAGGCCCGAGCGCTTCCAGACGTGCCCCGACGCCTTCGACCTGATCGTCACT
TGTGAAGAGCGAGTCTACGACCAGGTGGTGGAG

Alignment

ORF - retro_tbel_2435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSLRVAVVCSSNQNRSMEAHNILSK-GFSVPSFGTGTHVKLPGPAP-NKPNVYDFKTTYGV---DLLRKD
          S.LRVAVVCS.NQNRSM.AHN.LSK.GF.V.SFGTGT.VKLPGPAP..KPNVYDF.TTY.....DLL.KD
Retrocopy STLRVAVVCSNNQNRSM*AHNLLSKRGFCVRSFGTGTRVKLPGPAP<DKPNVYDFHTTYDQMYKDLLHKD

Parental  KELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVE
          ..LYT.NG.LHML.RNKRIKPRPERFQ.C.D.FDLI.TCEERVYDQVVE
Retrocopy EKLYTRNGVLHMLGRNKRIKPRPERFQTCPDAFDLIVTCEERVYDQVVE

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_2435 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2435 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013736	3 retrocopies	retro_amel_1930, retro_amel_292, retro_amel_84,
Erinaceus europaeus	ENSEEUG00000010799	1 retrocopy	retro_eeur_648,
Felis catus	ENSFCAG00000003318	1 retrocopy	retro_fcat_54,
Microcebus murinus	ENSMICG00000011016	5 retrocopies	retro_mmur_1057, retro_mmur_1081, retro_mmur_1353, retro_mmur_890, retro_mmur_891,
Mustela putorius furo	ENSMPUG00000014394	2 retrocopies	retro_mputfur_108, retro_mputfur_1408,
Sarcophilus harrisii	ENSSHAG00000009747	1 retrocopy	retro_shar_32,
Tupaia belangeri	ENSTBEG00000010136	3 retrocopies	retro_tbel_1675, retro_tbel_2435 , retro_tbel_2704,