RetrogeneDB ID: retro_tbel_4316

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_76419:251..1552(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIF1A
• Ensembl ID: ENSTBEG00000011941
• Aliases: None
• Description: hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) [Source:HGNC Symbol;Acc:4910]

Sequence

>retro_tbel_4316
ATTACTGAATTGATGGGTTATGAGCCAGAAGAACTTTTGGGCTGCTCAATTTATGAATATTATCATGCTCTGGATTCTGA
TCATCTGACCAAAACTCATCATGATATGTTTACTAAAGGACAAGTCACCACAGGACAGTACAGGATGCTTGCCAAGAGAG
GTGGATATGTCTGGGTTGAAACTCAAGCAACTGTCATATATAACACTAAGAACTCTCAACCACAATGCATCATGTGTGTA
AATTATGTTGTAAGTGGTATTATTCAGCACGACTTGATTTTCTCCCTTCAACAAACAGAATGTGTCCTCAAACCGGTTGA
ATCTTCAGATATGAAAATGACTCAGCTATTCACCAAAGTTGAATCAGAAGACACAAGTAGCCTTTTTGATAAACTTAAGA
AGGAACCTGATGCTTTAACTTTGCTGGCCCCAGCTGCTGGAGACACAATCATATCTTTAGATTTTGGCAGCAATGACACA
GAAACTGATAACCAACAACTTGAGGAAGTTCCATTGTATAACAATGTAATGCTCCCTTCATCCAATGAAAAGTTACAAAA
CATAAATTTGGCAATGTCTCCATTACCTGCATCTGAAACTCCAAATCCACTTTGAAGTAGTGCTGACCCTGCACTCAGTC
AAGAAGTTGCATTAAAATTAGAACCAAATCCAGAGTCATTGGAACTTTCTTTTACTATGCCCCAGATTCAAGATCAGCCA
GCCAGCCATTCCTTCTGATGGAAGCATTAGGCAAAGTTCACCTGAGCCTAACAGTCCCAGTGAACATTGTTTTTATGTGG
ACAGTGATATGGTCTATGAATTCAAGTTGGAATTGGTAGAAAAACTTTTTGCTGAAGACACAGAAGCAAAAAATCCATTT
TCCACTCAGGACACTGACTTAGACCTGGAGATGTTAGCCCCCTATATCCCAATGGATGATAACTTCCAATTACGCTCCTT
CGATCAACTGTCAACATTAGAAAGCAGCTCTTCAAGCCCTCAAAGTGTGAGCAGCACAATTCCAGTATTCCAGCAGACTC
AAATGCAAGAACCTGCTATTAACACTACCAAGACCACTGCATGAATTAAAAACTGTGACCAAAGATGGTATGGAAGATGT
TAAAATACTGGTTTCATCTCCTACTCATATACCTAAAGAAACTACTAGTGCCACAACATCACCATATAAAGATGCTCAAA
GTCAGACAGCCTCACCAAACAGAGCAGGAAAAGTAGTCATAGAACAGACAGAAAAATCTCATCCAAGAAGCCCTAATGTG
TTATCTGTCACTTTGAGTCAA

Alignment

ORF - retro_tbel_4316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.73 %
• Parental protein coverage: 53.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ITELMGYEPEELLGRSIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVETQATVIYNTK
          ITELMGYEPEELLG.SIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVETQATVIYNTK
Retrocopy ITELMGYEPEELLGCSIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVETQATVIYNTK

Parental  NSQPQCIVCVNYVVSGIIQHDLIFSLQQTECVLKPVESSDMKMTQLFTKVESEDTSSLFDKLKKEPDALT
          NSQPQCI.CVNYVVSGIIQHDLIFSLQQTECVLKPVESSDMKMTQLFTKVESEDTSSLFDKLKKEPDALT
Retrocopy NSQPQCIMCVNYVVSGIIQHDLIFSLQQTECVLKPVESSDMKMTQLFTKVESEDTSSLFDKLKKEPDALT

Parental  LLAPAAGDTIISLDFGSNDTETDDQQLEEVPLYNDVMLPSSDEKLQNINLAMSPLPASETPKPLRSSADP
          LLAPAAGDTIISLDFGSNDTETD.QQLEEVPLYN.VMLPSS.EKLQNINLAMSPLPASETP.PL.SSADP
Retrocopy LLAPAAGDTIISLDFGSNDTETDNQQLEEVPLYNNVMLPSSNEKLQNINLAMSPLPASETPNPL*SSADP

Parental  ALNQEVALKLEPNPESLELSFTM-PQIQ-DQPASPSDGSTRQSSPEPNSPSEYCFYVDSDMVNEFKLELV
          AL.QEVALKLEPNPESLELSFTM.P.....QPA.PSDGS.RQSSPEPNSPSE.CFYVDSDMV.EFKLELV
Retrocopy ALSQEVALKLEPNPESLELSFTM>PRFKISQPAIPSDGSIRQSSPEPNSPSEHCFYVDSDMVYEFKLELV

Parental  EKLFAEDTEAKNPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSTLESSSSSPQSVSSTIPVFQQTQMQ
          EKLFAEDTEAKNPFSTQDTDLDLEMLAPYIPMDD.FQLRSFDQLSTLESSSSSPQSVSSTIPVFQQTQMQ
Retrocopy EKLFAEDTEAKNPFSTQDTDLDLEMLAPYIPMDDNFQLRSFDQLSTLESSSSSPQSVSSTIPVFQQTQMQ

Parental  EPAINTTKTTATP-DELKTVTKDGMEDVKILVASPSPTHIPKETTSATTSPYKDTQSRTASPNRAGKGVI
          EPAIN...TT.T...ELKTVTKDGMEDVKILV.SP..THIPKETTSATTSPYKD.QS.TASPNRAGK.VI
Retrocopy EPAIN---TTKTT>HELKTVTKDGMEDVKILVSSP--THIPKETTSATTSPYKDAQSQTASPNRAGKVVI

Parental  EQTEKSHPRSPNVLSVTLSQ
          EQTEKSHPRSPNVLSVTLSQ
Retrocopy EQTEKSHPRSPNVLSVTLSQ

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_4316 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4316 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000011941	1 retrocopy	retro_tbel_4316 ,