RetrogeneDB ID: retro_tbel_3501

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_142924:67083..67649(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSTBEG00000007283
• Aliases: None
• Description: transcriptional adaptor 1 [Source:HGNC Symbol;Acc:30631]

Sequence

>retro_tbel_3501
AGCAAGGAAGAGTTTGACCTTGAAGTTCACAAACTTCTTACCCAGGACAATGTCCTCTCTCACGACTTCCTCCTGGCCAT
TCTCACGTGCTGTCAGATTTTGGTTTCTATACCAGAGGATGCTGGATCTTGGCCCTGGACAGGGACCTCTGCAGCCAAGC
CTGGACAAAACAAGGGAAAGAAAAATACCTCTTCTGTTTGTCAGAAATTTGATCATGGATTCCAGCCTCAAAATCCTCTC
TTGGGAGCCCAACAGTTTCTGGCAGAAGATCCCCAAGATGATGACTAGTTGAAATTTTGTTCCCACACAATGATGCTTTC
TACTCAGGGTCAGCTGGAAGGGAGAATGATAGTGACCGCTTATGAGCATGGGCTGGATAATGTCATCGAGGCCATGTCAG
CTGTGGTCTATGCAGTGGAGAATCACCGTAAAGATATACTGACACCAGTTGTGTCAGGAAGGGAGGCTTATGGGTCGCAA
ATAATCATTTTAAATAAGCCTTTGGCAGTAACATGATGCTACAGCCACACCTGAAGAACAGCATAAGAGCTTACAACAAC
CTCATA

Alignment

ORF - retro_tbel_3501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 57.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKEEFDLEAHRLLTQDNVHSHNDFLLAILTRCQILVSTPEGAGSLPWTGGSAAKPGKPKGKKKISSVRQK
          SKEEFDLE.H.LLTQDNV.SH.DFLLAILT.CQILVS.PE.AGS.PWTG.SAAKPG..KGKK..SSV.QK
Retrocopy SKEEFDLEVHKLLTQDNVLSH-DFLLAILTCCQILVSIPEDAGSWPWTGTSAAKPGQNKGKKNTSSVCQK

Parental  FDHRFQPQNPLSGAQQFVAKDPQDDDDLKLCSHTMMLPTRGQLEGRMIVTAYEHGLDNVTEEAVSAVVYA
          FDH.FQPQNPL.GAQQF.A.DPQDDD.LK.CSHTMML.T.GQLEGRMIVTAYEHGLDNV..EA.SAVVYA
Retrocopy FDHGFQPQNPLLGAQQFLAEDPQDDD*LKFCSHTMMLSTQGQLEGRMIVTAYEHGLDNVI-EAMSAVVYA

Parental  VENHLKDILTSVVSRRKAYR-LRDGHFKYAFGSNVTPQPYLKNSVAAYNTLI
          VENH.KDILT.VVS.R.AY......HFK.AFGSN...QP.LKNS..AYN.LI
Retrocopy VENHRKDILTPVVSGREAYG<VANNHFK*AFGSNMMLQPHLKNSIRAYNNLI

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_3501 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3501 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501 ,