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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagacacttgtaaattgtgtacttggactactttatcacgcagtctgttggataatatctagtttttgacgtatgatcatttgttttagtttgagcagGTTGGCATTGCGAATACAGGCTATGTTGAGACTCATGATGTTCATGGCTTAGTTGCACCCAGAGGACTGTCAGGAGATTCATTGAAGAGGTTACCCCACC

Basic information

species Glycine max
transcript GLYMA17G11000.2
intron # 3
splice site 3'
intron type U2

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|151407124|gb|EV276939.1|EV276939
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151407124|gb|EV276939.1|EV276939
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151407124|gb|EV276939.1|EV276939
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151407124|gb|EV276939.1|EV276939
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192303939|gb|FG995253.1|FG995253
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192303939|gb|FG995253.1|FG995253
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192303939|gb|FG995253.1|FG995253
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192303939|gb|FG995253.1|FG995253
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192311811|gb|FK004918.1|FK004918
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192311811|gb|FK004918.1|FK004918
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192311811|gb|FK004918.1|FK004918
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192311811|gb|FK004918.1|FK004918
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192300820|gb|FG991157.1|FG991157
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192300820|gb|FG991157.1|FG991157
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192300820|gb|FG991157.1|FG991157
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192300820|gb|FG991157.1|FG991157
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192301869|gb|FG995487.1|FG995487
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192301869|gb|FG995487.1|FG995487
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192301869|gb|FG995487.1|FG995487
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192301869|gb|FG995487.1|FG995487
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192308291|gb|FK000871.1|FK000871
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192308291|gb|FK000871.1|FK000871
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192308291|gb|FK000871.1|FK000871
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192308291|gb|FK000871.1|FK000871
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|298193614|gb|HO040262.1|HO040262
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         GTTGGCATTGCGAATACAGGCTATGTTGAGACTCATGATGTTCATGGCTTA
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcagGTTGGCATTGCGAATACAGGCTATGTTGAGACTCATGATGTTCATGGCTTA
EST: gi|192311812|gb|FK004919.1|FK004919
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGTTTGAGCAG                 
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTAC-A-----A-TTT--GCAGgtaattctcc ... gt
EST: gi|192330266|gb|FK019846.1|FK019846
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192330266|gb|FK019846.1|FK019846
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192330266|gb|FK019846.1|FK019846
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|192330266|gb|FK019846.1|FK019846
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151398809|gb|EV268680.1|EV268680
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151398809|gb|EV268680.1|EV268680
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151398809|gb|EV268680.1|EV268680
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-
EST: gi|151398809|gb|EV268680.1|EV268680
EST:     TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAG                         T
genomic: TTGTTGAGGAATCCCTTACACCTGCTATTTTAACTGCTTACAATTTGCAGgtaattctcc ... gtttgagcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttggataatatctagtttttgacgtatgatcatttgttttagtttgagcagGTTGGCATTGCGAATACAGGCTATGTTGAGACTCATGATGTTCATGGCTTAGTTGCACCCAGAGGACTGTCAGGAGATTCATTGAAGAGGTTACCCCACC
                    ttttgac  putative branch site (score: 3)
        ataatatctagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagacacttgtaaattgtgtacttggactactttatcacgcagtctgttggataatatctagtttttgacgtatgatcatttgttttagtttgagcagGTTGGCATTGCGAATACAGGCTATGTTGAGACTCATGATGTTCATGGCTTAGTTGCACCCAGAGGACTGTCAGGAGATTCATTGAAGAGGTTACCCCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - cacttgt
- - - - - - - - -tgtgtac
- - - - - - - - - - - - - - - - - - - cacgcag
- - - - - - - - - - - - - - - - - - - - - - -tctgttg