RetrogeneDB ID: retro_tbel_89

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1083:177399..177991(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000002194
• Aliases: None
• Description: None

Sequence

>retro_tbel_89
ATGAAGAGTGTGGTCTACCGTGCTTTTTCTCAGAAAGAGGCAAGAGAGTCCGATGTTCAGCATACAGGAACTGTGTGGGC
CGAGGCCTTTGTGAAGGCCTTCCTGAAGCACAGCGTGCCCCGCATGAGCCAGCAAGCCCTGGAGGACCTGCTGCAGTGCA
AGGCCGTTACTCTAGAGTATTTCACTTGCTGGAAGAGAAAGGAGAAGAAAGAGAAAACCAAAGGCCTCTCTGCCAGGCAG
AGGAGGTAACTGTGGCTCTTTGACATTAAGCCAGAGCAACAGAAATACAATCTTTTTCTCCAGCTGCATGAACTTTGGAA
GCAGTACATCCGGGACCTGTGCAATGGTCTCAAGCCAGACACGCAGCCACAGATGATTCAAGCCAAGCTGTTAAAGGCAG
ATCTTTGTGGTGCTATTATTTCAGTCCACAAAATCCAGATGCCCCTCATATGTGGGTGTTACAAGAATTTTTCTACAGGA
AACCAAGGCTTTCGAAATTATCACCAAAGAGGACCACCTGAAAGTTATCCCCAAGCTAAATTGTGTGTTCACTGTGGAAA
TCATGACTTTTAAAGAGCTGGTTCAGCCAAGT

Alignment

ORF - retro_tbel_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 90.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSVVYRAFSQKEAKEFDVQHAGVARAEAFVKAFLKRSVPRMSQQALEDQLQRKAVILEYFTRRRKRKEK
          MKSVVYRAFSQKEA.E.DVQH.G...AEAFVKAFLK.SVPRMSQQALED.LQ.KAV.LEYFT...KRKEK
Retrocopy MKSVVYRAFSQKEARESDVQHTGTVWAEAFVKAFLKHSVPRMSQQALEDLLQCKAVTLEYFTCW-KRKEK

Parental  KKKSKGLSARQRRELRLFDIKPEQQRYSLFLPLHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADLHGAI
          K.K.KGLSARQRR.L.LFDIKPEQQ.Y.LFL.LHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADL.GAI
Retrocopy KEKTKGLSARQRR*LWLFDIKPEQQKYNLFLQLHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADLCGAI

Parental  ISV-TKSKCPSYVGVTGILLQETKHVFKIITKEDRLKVIPKLNCVFTVEIDDFVSYIYGS
          ISV.TKS.CPSYVGVT.I.LQETK..F.IITKED.LKVIPKLNCVFTVEI..F......S
Retrocopy ISV>TKSRCPSYVGVTRIFLQETK-AFEIITKEDHLKVIPKLNCVFTVEIMTFKELVQPS

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_89 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_89 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008041	1 retrocopy	retro_mputfur_1088,
Oryctolagus cuniculus	ENSOCUG00000015974	1 retrocopy	retro_ocun_1367,
Otolemur garnettii	ENSOGAG00000011168	2 retrocopies	retro_ogar_3293, retro_ogar_541,
Sorex araneus	ENSSARG00000004748	1 retrocopy	retro_sara_410,
Tupaia belangeri	ENSTBEG00000002194	6 retrocopies	retro_tbel_1225, retro_tbel_1516, retro_tbel_2043, retro_tbel_3671, retro_tbel_3821, retro_tbel_89 ,