RetrogeneDB ID: retro_tbel_2704

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_117091:46733..47093(+)
• Located in intron of: ENSTBEG00000004901

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_2704
ATGCCGTTGCCGCTGCGGGTGGCCGTGGTGTGCTCCAGCAACCAGAACCGGAGCATGGAGGCGCACAGCATCCTCAGCAA
ACGCGGCTTCAGCGTGCGCTCCTTCGGCACCGGCACCCACGTGAAGCTGCCGGGGGCCGCGCCCGACAAGCCCAACGTCT
ACGACTTCAGAACCACCTACGACCAGATGTACCACGACCTCCTGAGGAAGGACAAGGAGCTCTACACCCAGAACGGCCTC
TTACACATGCTGGACAGAAACAAGAGGATCAAGGCCGCGCGGGAGAGGTTCCAGAGCTGCAGGGACGTGTTCGACCTGAT
CGTCACGTGCGAGGAGCGCGTCTACGACCAGGTGGTGGAG

Alignment

ORF - retro_tbel_2704 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSSLRVAVVCSSNQNRSMEAHNILSK-GFSVPSFGTGTHVKLPGPAPNKPNVYDFKTTYGV---DLLRK
          MP..LRVAVVCSSNQNRSMEAH.ILSK.GFSV.SFGTGTHVKLPG.AP.KPNVYDF.TTY.....DLLRK
Retrocopy MPLPLRVAVVCSSNQNRSMEAHSILSKRGFSVRSFGTGTHVKLPGAAPDKPNVYDFRTTYDQMYHDLLRK

Parental  DKELYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVE
          DKELYTQNG.LHMLDRNKRIK...ERFQ.C.D.FDLI.TCEERVYDQVVE
Retrocopy DKELYTQNGLLHMLDRNKRIKAARERFQSCRDVFDLIVTCEERVYDQVVE

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_2704 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2704 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 ,