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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctaccacaaaaattgcatttaccatgccctcccctcaaatctcaaatctcaaatctcaaatttcaactcatgtttgccacaattttgactagtaattttaaaattgaaaaggggtgaagcatggtattaaattgaacatacatacctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGCATATGGGAATGTTGTGAACTCCTTAATGAAGTGGTGGATGAGAGTGACC

Basic information

species Glycine max
transcript GLYMA08G21300.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21300.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02940.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcatctaccacaaaaattgcatttaccatgccctcccctcaaatctcaaatctcaaatctcaaatttcaactcatgtttgccacaattttgactagtaattttaaaattgaaaaggggtgaagcatggtattaaattgaacatacatacctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGCATATGGGAATGTTGTGAACTCCTTAATGAAGTGGTGGATGAGAGTGACC
                                             ||  ||   ||   || |||||| ||||  |||   |     |||||    ||  | |||||   |  |||| |     |  | |||  ||  |||     ||  |||      ||||||||||||||||||||||||||   |   ||||||||||  | ||||||||||||||||| |||||||| || ||||| || || ||||| ||||| |
----------------------------------------gtgagaagatcgcctc---aacctcaaaattca--tcagactctgagcaatt----cttttcattttgtcagagaaatgaatcaatccttggcctttgatt---tttatgtact-----agGTGAAGAAAATGAGAGAGGAGTACAGCAGGCTGAACAGGGTGCAAATGAGCATATGGGAATGCTGTGAACTTCTCAATGATGTTGTTGATGAAAGTGATC
















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|192310996|gb|FK001605.1|FK001605
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGGGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|15204297|gb|BI427065.1|BI427065
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|151397267|gb|EV267140.1|EV267140
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|13312797|gb|BG406448.1|BG406448
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|22540966|gb|BU090809.1|BU090809
EST:     GAGTGGAGAACTTCTACAGAAAAGATGACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|254329842|gb|GR839395.1|GR839395
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAA-TGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|151396455|gb|EV266332.1|EV266332
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|163921518|gb|EH039303.1|EH039303
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
EST: gi|192295399|gb|FG987013.1|FG987013
EST:     GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTC                         GTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC
genomic: GAGTGGAGAACTTCTACAGAAAAAATCACACTTACCAATCAATTGATTTCgtaagcatct ... acctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaattgaaaaggggtgaagcatggtattaaattgaacatacatacctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGCATATGGGAATGTTGTGAACTCCTTAATGAAGTGGTGGATGAGAGTGACC
                          tattaaattgaacata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatctaccacaaaaattgcatttaccatgccctcccctcaaatctcaaatctcaaatctcaaatttcaactcatgtttgccacaattttgactagtaattttaaaattgaaaaggggtgaagcatggtattaaattgaacatacatacctatacagGTGAAGAAAATGAGAGAGGAGTACGCAAAATTGAACAGGGTAGAGATGAGCATATGGGAATGTTGTGAACTCCTTAATGAAGTGGTGGATGAGAGTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA