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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGTCCACGGTGATGAATTTGAGTACAATGATCCTGTGGATGGTTCCATCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttactgcttgagaaatattggttacaattaacttaatggaaaaaagctgaaatttcgtgtggtggtctttcagaattgaaaatgcatcttcttg...

Basic information

species Glycine max
transcript GLYMA08G04890.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 16
TGTTGTCCACGGTGATGAATTTGAGTACAATGATCCTGTGGATGGTTCCATCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttactgcttgagaaatatt-------ggttacaattaacttaatggaaaaaagctgaaatttcgtgtgg--tggtctttcagaattgaaaatgcatcttcttg---
 || | |   | ||||||||| |||||||| ||||| || ||||| ||||| ||    || ||||||||||| || |||||||| || ||||||||| | || |||   ||  ||      ||||       || |||| |  |  |||    |||  | |  || |          |  || |      ||  |  || | |    ||   
CGTCGCCAGTGCTGATGAATTCGAGTACAAAGATCCAGTTGATGGATCCATTTCGAAGCACCAGGGAATCCGTTACTTGTTTGAAGACGGATCACGACTTgtaagtcatctttttcttcggtatttgagcttggatacattccagctaagaacaaagtgatagaaatcaaaactaactaatcctctcttgttatatctgaaaccatatgaag

upper sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 17
TGTTGTCCACGGTGATGAATTTGAGTACAATGATCCTGTGGATGGTTCCATCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttactgcttgagaaatattggttacaattaacttaatggaaaaaagctgaaatttcgtgtggtggtctttcagaattgaaaatgcatcttcttg----
|||||   | | |||||||||||| ||||| |||||||| |||||||||||||||   |||||||| || |||||| ||||||| ||||| ||||||||||| |||    | | |     || |   ||   |||   ||        ||   | | | ||    || |  |  |   |||    |||||   ||         
TGTTGCGAAAGCTGATGAATTTGAATACAAAGATCCTGTTGATGGTTCCATCTCAAAGCATCAGGGTATTCGATATATGTTTGAAGATGGGTCACGATTGgtaagtaggtttcctttatcatttcttttgggattgcattggctactgaactttcagaatt-acctgatacttatagggaac---aaatgttcctagagataca
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|22932077|gb|BU549216.1|BU549216
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|58019793|gb|CX706535.1|CX706535
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|19269460|gb|BM885716.1|BM885716
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|6567204|gb|AW234815.1|AW234815
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|12690328|gb|BG156664.1|BG156664
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|12691027|gb|BG157363.1|BG157363
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGGTGCAACAATTCGATTATA
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGG-TGCAACAATTCGATTATA
EST: gi|193597826|gb|FK549232.1|FK549232
EST:     ATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: ATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|6725125|gb|AW309524.1|AW309524
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGG-ACNTGGATCAGAAGGTGCAACAATTCGATTATA
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAAC-TGGATCAGAAGGTGCAACAATTCGATTATA
EST: gi|58015854|gb|CX702596.1|CX702596
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|151406289|gb|EV276104.1|EV276104
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|57574755|gb|CX547730.1|CX547730
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|13789290|gb|BG651881.1|BG651881
EST:     TTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
EST: gi|120530798|gb|EH258931.1|EH258931
EST:     TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTG                         ATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC
genomic: TCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttac ... actactatagATTTTCCGCCTATCTGGAACTGGATCAGAAGGTGCAACAATTCGATTATAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGTCCACGGTGATGAATTTGAGTACAATGATCCTGTGGATGGTTCCATCTCATCACATCAGGGAATCCGATATTTGTTTGAGGATGGATCACGATTGgtgagtttactgcttgagaaatattggttacaattaacttaatggaaaaaagctgaaatttcgtgtggtggtctttcagaattgaaaatgcatcttcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggtgg