RetrogeneDB ID: retro_tbel_3170

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_132800:35893..36431(-)
• Located in intron of: None

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_3170
GTGACAGTTTGTGATGCGATAAATCAAGGTATGGCTGAGCTGGGAAGAGATGAGAGGGTATTTCTGCTTGGGGAAGAAGT
CGCCCAGTATGATGGGGCATACAATGTGAGTCGAGGTCTCTGGAAGAAGTTCGGAGACGAGAGGATCATAGGCACTCCCA
TCTCCGAGATGGGCTTTGCTCGAAGTGCCGTAGAGGCAGCTAGGGCTGGGTTGTGACCCATTTGTGAATTTATGACCTTC
AATTTCTCCATGCAAGCCATTGGCCAGGTTATAAATTCAGCTGCCAAGACGTATTGCATGTGGGGGGCCTTCAGCCTGTT
CCCATCTTCTTCAGGGGACCCGACGGCGCCGGGTCAATGTAGCTGCCTGGCACTCCCAGTGCTTTGCTCCGTGGTATGGG
CACTGTCCAGGCTTACAGGTGGTCAGCCCCTGGAGCTCAGAGGATGCGAAAGGACTTATAAAATCAGGCATCCGGGATAA
TCATCCAGTGGTGGTGCTGAAGAATGAACTGATGTATGGAGTTCCCGTGAATTTCCCA

Alignment

ORF - retro_tbel_3170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 55.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAVRDALNQAKEEELEKDEKVFLL-EEVAQYDGAYKVSRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMA
          V.V.DA.NQ...E.L..DE.VFLL.EEVAQYDGAY.VSRGLWKK.GD.RII.TPISEMGFA..AV.AA.A
Retrocopy VTVCDAINQGMAE-LGRDERVFLLGEEVAQYDGAYNVSRGLWKKFGDERIIGTPISEMGFARSAVEAARA

Parental  GLRPICEFMTFNFSMQAIDQVINSAAKTCYM-SGGLQCVPIVFRGPNGASA-GVAAQHSQCFAAWYGHCP
          GL.PICEFMTFNFSMQAI.QVINSAAKT..M..GGLQ.VPI.FRGP.GA....VAA.HSQCFA.WYGHCP
Retrocopy GL*PICEFMTFNFSMQAIGQVINSAAKTYCM<VGGLQPVPIFFRGPDGAGS<NVAAWHSQCFAPWYGHCP

Parental  GLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVPFEFP
          GL.VVSPW.SEDAKGLIKS.IRDN.PVVVL.NELMYGVP..FP
Retrocopy GLQVVSPWSSEDAKGLIKSGIRDNHPVVVLKNELMYGVPVNFP

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_3170 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3170 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 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 ,