RetrogeneDB ID: retro_tbel_3669

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148120:56112..56685(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000009617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX19B
• Ensembl ID: ENSTBEG00000009816
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B [Source:HGNC Symbol;Acc:2742]

Sequence

>retro_tbel_3669
TGTCTGTGCTTCTCCTCAATATATGAGCTCGCCCTCCAAGCGAGAAAAGTGATTAAACAAATGAACAAATTTTACCCTGA
ACTGAAGCTAGCTTATGCTGTTCGAGGCAATAAATTGGAAAGAGATCAGAAGATCAGTGAATAGATTGTCATTGGCCCTC
CTGGGACCGTCCTGGACTGGTGCTCCAAACTCAAGTTCATTGACCCCAAGAAGATCAAGGTGTTTGTCCTGGACTAGGCT
GACATGATGATAACTACTCAGTGCCACCAAGACCAGAGCATCCGCATCCAGAGGATGCTGCCCAGAAACTGCCAGATGCT
ACTGTTCTCAGCGACCTTCGAAGACTCTGTGTGAAAGTTTGCCCAGAAGGTGGTCCCAGACCCCAATGTCATCAAACTGA
AGCACGAGAAGGAGACCCTGGACACCATCAAGTAGTATTACGTCCTGTGAAACAACCCGGACGAGAAGTTTCAGGCCCTG
TAACCTGTACAGTCCATCACCATCGCACAAGCCATGATCTTCTGGCACACCCACAAAACAGCGAGTTGGCTGGCAACAGA
GTTGTCGAAAGAA

Alignment

ORF - retro_tbel_3669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• Parental protein coverage: 74.42 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPK
          CLC.S..YELALQ..KVI.QM.KFYPELKLAYAVRGNKLER.QKISE.IVIG.PGTVLDWCSKLKFIDPK
Retrocopy CLCFSSIYELALQARKVIKQMNKFYPELKLAYAVRGNKLERDQKISE*IVIGPPGTVLDWCSKLKFIDPK

Parental  KIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETL
          KIKVFVLD.AD.MI.TQ.HQDQSIRIQRMLPRNCQMLLFSATFEDSV.KFAQKVVPDPNVIKLK.E.ETL
Retrocopy KIKVFVLD*ADMMITTQCHQDQSIRIQRMLPRNCQMLLFSATFEDSV*KFAQKVVPDPNVIKLKHEKETL

Parental  DTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKE
          DTIK.YYVL.NN.DEKFQAL......ITIAQAMIF.HT.KTASWLA.ELSKE
Retrocopy DTIK*YYVL*NNPDEKFQAL*PVQ-SITIAQAMIFWHTHKTASWLATELSKE

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_3669 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3669 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010216	1 retrocopy	retro_chof_106,
Ictidomys tridecemlineatus	ENSSTOG00000025733	1 retrocopy	retro_itri_1877,
Tupaia belangeri	ENSTBEG00000009816	1 retrocopy	retro_tbel_3669 ,