RetrogeneDB ID: retro_tbel_4523

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_88201:8830..9731(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEAD1
• Ensembl ID: ENSTBEG00000017462
• Aliases: None
• Description: TEA domain family member 1 (SV40 transcriptional enhancer factor) [Source:HGNC Symbol;Acc:11714]

Sequence

>retro_tbel_4523
GTGTCTAGTCACATTCAGGTTCTTGCCAGAAGGAAATCTCGTGATTTTCATTCCAAGCTAAAGGATCAGACTGCAAAGGA
TAAGGCCCTGCAGCACACGGCAGTCATGTCTTCAGCCCAGATCATCTCAGCCACTGCCATTCACAAAAAGCTGGGGCTGC
CCGGGATTCCACGCCCACCCTTCCTGGGGGCGCCAGGGTTCTGGCCAGGAATGATACAAACAGGGCAGCCAGGATCCTCA
CAAGACGCCAAGCCTTTCATGCAACAGGCCTACCCTATCCAGTCAGCGGTCACAGCTCCCATTCCAGGGTTTGAGCCTGC
ATCAGCCCCAGCTCCCTCAGTCCCTGCCCGGCAGAGCCACTCTATTGGCACAGCCAAGCTTCTCCTGGTGGAGTTTTCAG
CTTTTCTTGAACTGAAGTGAGACCCAGACTCGTACAACAAACACCTCTTCGTGTACATTGGGCATGCCAACCATTCGTAC
AGTGACCCTTTGCTCAAATTGGTGGACATTCATCAGATTTATGACAAATTTCCTGAAAAGAAAGCTGACTTGAAGGAACT
ATTTGGAAAGGGCCCTCAAAATGCCTTCTTCCTCGTAAAATTCTGGGCTGATTTAAACTGCAATTTTCAAGACGATGCCG
GGGCTTTTTAATGGTGTAACCAGCCAGTATGAGAGTTCTGAAAATATGACAGTCACCTGTTCCACCAAAGTTTGCTCCTT
CGAGAAGCAAGTAGTAGAAAAAGTAGAGACCGAGTACACAAGGTTTGAGAATGGCCGATTTGTGTACCAAATAAACCGCT
CCCCGACGTGTGAATACATGATCAACTTCATCCACAAGCTCAAACACTTACCAGAGAAATATATGATAAACAGTGTTTTG
GAAAACTTCACCATTTTATTG

Alignment

ORF - retro_tbel_4523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 77.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSSHIQVLARRKSRDFHSKLKDQTAKDKALQHMAAMSSAQIVSATAIHNKLGLPGIPRPTFPGAPGXXXX
          VSSHIQVLARRKSRDFHSKLKDQTAKDKALQH.A.MSSAQI.SATAIH.KLGLPGIPRP.F.GAPG....
Retrocopy VSSHIQVLARRKSRDFHSKLKDQTAKDKALQHTAVMSSAQIISATAIHKKLGLPGIPRPPFLGAPGFWPG

Parental  XXXXXXXXXXXXVKPFVQQAYPIQPAVTAPIPGFEPASAPAPSVPAWQGRSIGTTKLRLVEFSAFLEQQR
          .............KPF.QQAYPIQ.AVTAPIPGFEPASAPAPSVPA.Q..SIGT.KL.LVEFSAFLE...
Retrocopy MIQTGQPGSSQDAKPFMQQAYPIQSAVTAPIPGFEPASAPAPSVPARQSHSIGTAKLLLVEFSAFLELK*

Parental  DPDSYNKHLFVHIGHANHSYSDPLLESVDIRQIYDKFPEKKGGLKELFGKGPQNAFFLVKFWADLNCNIQ
          DPDSYNKHLFV.IGHANHSYSDPLL..VDI.QIYDKFPEKK..LKELFGKGPQNAFFLVKFWADLNCN.Q
Retrocopy DPDSYNKHLFVYIGHANHSYSDPLLKLVDIHQIYDKFPEKKADLKELFGKGPQNAFFLVKFWADLNCNFQ

Parental  DDAGA-FYGVTSQYESSENMTVTCSTKVCSFGKQVVEKVETEYARFENGRFVYRINRSPMCEYMINFIHK
          DDAGA.F.GVTSQYESSENMTVTCSTKVCSF.KQVVEKVETEY.RFENGRFVY.INRSP.CEYMINFIHK
Retrocopy DDAGA>FNGVTSQYESSENMTVTCSTKVCSFEKQVVEKVETEYTRFENGRFVYQINRSPTCEYMINFIHK

Parental  LKHLPEKYMMNSVLENFTILL
          LKHLPEKYM.NSVLENFTILL
Retrocopy LKHLPEKYMINSVLENFTILL

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_4523 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4523 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010263	1 retrocopy	retro_cjac_193,
Tupaia belangeri	ENSTBEG00000017462	1 retrocopy	retro_tbel_4523 ,
Tarsius syrichta	ENSTSYG00000001514	1 retrocopy	retro_tsyr_657,
Tursiops truncatus	ENSTTRG00000006621	1 retrocopy	retro_ttru_1096,