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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgtattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG

Basic information

species Glycine max
transcript GLYMA12G31740.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgtattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG
                                                 ||  | || | || ||| ||              |   | ||| |||||  | |  | ||||  |||| ||    ||| || | |  | || |||  |||||||||   |||||  || || |||  || ||||| |||||||||||||| || ||||||||||| ||||| ||||||
--------------------------------------------gtaagcttcctaccactgttagctttcgttgccaagttgtaattatttgggtttcgttt--gatttgtttttggat----cagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgt-attattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG
                    | | |    |        |       |  ||       |||  |  || ||   ||      |||  || ||    ||||  | |  |||   ||| | |  || ||| |||  |  | | || || ||||||||  | ||||| |||||  |||| || |||||||| ||||||||||| ||||| ||||||||||| || || |||
-------------------gtaagtttttcttaataaacaatttttccgctgc-----attaat--ttcagaatttgctgtgtttaatcatt---gttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
















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|192330947|gb|FK021660.1|FK021660
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|192306233|gb|FG996847.1|FG996847
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|192330326|gb|FK019876.1|FK019876
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|10233586|gb|BE802474.1|BE802474
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|151411977|gb|EV281788.1|EV281788
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|192328346|gb|FK020057.1|FK020057
EST:     ATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCGGCACTTTTCTTTCAATACAGTACTGCACTGGGACC
genomic: ATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|13790864|gb|BG653455.1|BG653455
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|151407416|gb|EV277231.1|EV277231
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|24205709|gb|BU964962.1|BU964962
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|13790863|gb|BG653454.1|BG653454
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|298179193|gb|HO027664.1|HO027664
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|298183536|gb|HO028749.1|HO028749
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|209717530|gb|BW679664.1|BW679664
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
EST: gi|151408961|gb|EV278769.1|EV278769
EST:     TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGT                         TCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC
genomic: TTGAACCCAGAAAAGAAGAATCTTATGAAGGAAAAGTTACCCAGAAATGTgtaagcttcc ... tattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttcccctttgctcttttggtttaatctgtggtttggatttgtattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG
                      gtttaat  putative branch site (score: 4)
                                        atttgtattattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgtattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG

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