RetrogeneDB ID: retro_tbel_1651

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5385:1056102..1056582(-)
• Located in intron of: ENSTBEG00000013304

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSTBEG00000016148
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_tbel_1651
AAAAGAGGAGAAGGTATTTTGTTTGGGGAAGAAGTTGCCCAGTATGATGGGGCATACAAGGTTAGTTGAGGCCTTTGGAA
AAGAATACAGAGACAAGAGGGTCATAGACACTTCCATCTCTGAGGTGGCAGTTGCTGGAACTGCTGTAGGGGCAGCTGTG
GCTGGGTTGTGACCCACTTGTGAACTTATGACCTTCAGTTTCTCCATGCAAGCCATGACCAGGTTAAAATCAGCTGCCAA
GACCTACTGCATGTCAGGGGCCTTCGGCCTGTTCCCATCGTCTTCAGGGGGCCCAACGGTGCCTCAGCGGGCATAGCCAC
CCAGCACTCCCAGTGCTTTGCTGCATGGTGGGGGCACTGTCCAGGCTTAAAGGTGGTCAGCCCCTGGAATTCAGAGGCTG
CGAAAGGACTTATGGAATCGGCCATTCAGGATAATCATCTGGTGATGGTGCTGATCTACAGAATTCCTTGTGAGTTTCCC

Alignment

ORF - retro_tbel_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 50.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKDEKVFLLEEVAQYDGAYKVSRGLWKK-YGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSM
          ...E.....EEVAQYDGAYKVS.GLWK..Y.DKR.IDT.ISE...AG.AVGAA.AGL.P.CE.MTF.FSM
Retrocopy KRGEGILFGEEVAQYDGAYKVS*GLWKR>YRDKRVIDTSISEVAVAGTAVGAAVAGL*PTCELMTFSFSM

Parental  QAIDQVINSAAKTCYMSG-GLQCVPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGL
          QA......SAAKT..MSG.GL..VPIVFRGPNGASAG.A.QHSQCFAAW.GHCPGLKVVSPWNSE.AKGL
Retrocopy QAMTR-LKSAAKTYCMSG<GLRPVPIVFRGPNGASAGIATQHSQCFAAWWGHCPGLKVVSPWNSEAAKGL

Parental  IKSAIRDNNPVVVLENELMYGVPFEFP
          ..SAI.DN..V.VL.....Y..P.EFP
Retrocopy MESAIQDNHLVMVL----IYRIPCEFP

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_1651 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1651 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651 , retro_tbel_3170,