RetrogeneDB ID: retro_tbel_3398

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139286:57972..58718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBCH
• Ensembl ID: ENSTBEG00000004132
• Aliases: None
• Description: 3-hydroxyisobutyryl-CoA hydrolase [Source:HGNC Symbol;Acc:4908]

Sequence

>retro_tbel_3398
GAGAAAATACTGAATGATGCCTTTGGTTCTTGCCAAAAACTGTACGTTGCACTTACTCATGGAAATACAATGGGTGGGGG
AGTTGGTCTCTCAGTCCATGGGCAATTCCGACTGGCTATGGAACAGACACTTTTTGCAATGCGAGAAAGAGCAATAGGAC
TATTCCCTGATGTGGGTGGAGGTTATTTCTTGCCAAGACTTCAAGGAAAACTTGGCTACTTCCTTGCATTAATAGGATTC
AAACTAAAAGGAAGAGATATATGCAGAGTAGGAATTATTACACACTTTATAGATTCTGAAAAGTTGGGGATTTTAGAGAG
AGATTTGTTAGCCTTGAAATCTCCTTCTAAAGAAAATGTTGCAAATGCCTTAGATACTCACCATGCAGAGTCCGAGACTG
ATCAAGACAAGTCTTTTATACTTGAGGAATACATCGATAAAATAAACAGTTGCTTTTCAGCCAATACCATAGAACAGTTT
ATTGAAAACTTACAGTAAGATGGTTCATCTTTCACCCTAGAGCTATCAAAGGTAATTAATAAAATATCTCCAACATCCCT
AAAGATCACACTAAGGCAACTTATGGAGGGATCTTCAAAGACCTTGCAAGAAGTGTTAACTATGGAATATCAGTTCAGTC
AAGTTCGTATGAGGGGCCATGACTTTTATGAAGGTGTTAGAACTGTTTTAATTGATAAGATCATCGTCCAAGGTGGAAAC
CAGCTGATCTGAAAGAAGTTACTGAT

Alignment

ORF - retro_tbel_3398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 65.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYILNNAIGSCQKPYVALIHGITMGGGVGLSVHGHFRVATEKTVFAMPETAIGLFPDVGGGYFLPRLQGK
          E.ILN.A.GSCQK.YVAL.HG.TMGGGVGLSVHG.FR.A.E.T.FAM.E.AIGLFPDVGGGYFLPRLQGK
Retrocopy EKILNDAFGSCQKLYVALTHGNTMGGGVGLSVHGQFRLAMEQTLFAMRERAIGLFPDVGGGYFLPRLQGK

Parental  LGYLLALTGFRLKGRDVCRAGIATHFIDSEKLGMLEEDLLSLKSPSKENVADVLDTYHAESKIDQDKSFI
          LGY.LAL.GF.LKGRD.CR.GI.THFIDSEKLG.LE.DLL.LKSPSKENVA..LDT.HAES..DQDKSFI
Retrocopy LGYFLALIGFKLKGRDICRVGIITHFIDSEKLGILERDLLALKSPSKENVANALDTHHAESETDQDKSFI

Parental  LEEHMDKINSCFSANTVEQIIENLQRDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEVLTMEY
          LEE..DKINSCFSANT.EQ.IENLQ.DGSSF.LE..KVINK.SPTSLKITLRQLMEGSSKTLQEVLTMEY
Retrocopy LEEYIDKINSCFSANTIEQFIENLQ*DGSSFTLELSKVINKISPTSLKITLRQLMEGSSKTLQEVLTMEY

Parental  QLSQACMXXXXXXXXXXXXLIDK-DQCPKWKPADLKEVTD
          Q.SQ..M............LIDK.D..P.WKPADLKEVTD
Retrocopy QFSQVRMRGHDFYEGVRTVLIDK<DHRPRWKPADLKEVTD

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_3398 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3398 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000003341	1 retrocopy	retro_fcat_890,
Homo sapiens	ENSG00000198130	1 retrocopy	retro_hsap_3285,
Gorilla gorilla	ENSGGOG00000004988	1 retrocopy	retro_ggor_1317,
Macaca mulatta	ENSMMUG00000007283	1 retrocopy	retro_mmul_2062,
Mus musculus	ENSMUSG00000041426	1 retrocopy	retro_mmus_294,
Nomascus leucogenys	ENSNLEG00000006646	1 retrocopy	retro_nleu_1351,
Pongo abelii	ENSPPYG00000013021	2 retrocopies	retro_pabe_2714, retro_pabe_2827,
Pan troglodytes	ENSPTRG00000012741	1 retrocopy	retro_ptro_2222,
Tupaia belangeri	ENSTBEG00000004132	1 retrocopy	retro_tbel_3398 ,