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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttactctattgatgtttcacatcttgtgtcttcgtcgatttaagtcccttcacttagtttcacacggtgacattagaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAGACAGCAACAATGCAAGACAGTGCAT

Basic information

species Glycine max
transcript GLYMA11G18760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18760.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------atttactctattgatgtttcaca---tcttgtgtcttcgtcgatt---taagtcccttcac-ttagtttcacacgg----tgacattagaactttcatttctat---------catacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAGACAGCAACAATGCAAGACAGTGCAT
                                                ||| |     ||||  ||| |     | ||  | |||| | | |     | |   ||| |  |  || |     |     |||  || |   | |||||  | |           ||||||| ||  |  ||||||| || || |||||||| ||| |||| ||||||||  |||||||||||||||||||||| ||||||||||||||||| ||  | |
gtataattgtttcttcgtatgatctctagatattactcagctatatccattgaaaaggttgaatttttatgagttattacgccttcttggctcacacaggcttctttaaatctgtcttgggtgaaagatgaagtttgttatctcattgttgtgttatcgtgtttacagATTCGATCGGTCATGGTAGAGAACATTGAGAAGATAATGGAAAGAGGTGATAGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGATAGCTCGT

upper sequence: GLYMA11G18760.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------------------------------atttactctattgatgtttcacatcttgtgtcttcgtcgat-ttaagtcccttcacttagtttcacacggtgacattagaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAGACAGCAACAATGCAAGACAGTGCAT
                                                                                                  |  | | | |||| ||||      || | | || ||  ||  | | |   || | |     | |    |||        |  |  |  | |  ||| ||||||||||| |||||||| || || |||||||| ||| |||||||||||||  ||||||| ||||||||||| || || |||||||||||||||||| | |
gcaagtatcattttgtcattgtgggggtttgtgcatgatttatgtgtatatgtgcaggagatgacctaatgcaacacttgtgtacatttctcacttgttacattatcttgaagttt-gttctttttctttttgttaatacttaatattttta-tggccatgatgttgtgctgacgacaactaaaaat-tgacattcagATACGCACCATCATGGTAGAAAACATTGAGAAGATACTGGAGAGAGGTGATAGGATTGAACTTCTTGTTGACAAAACTGCAACAATGCAAGACAGTTCTT
















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|298197870|gb|HO039409.1|HO039409
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAA
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAA
EST: gi|19270491|gb|BM886747.1|BM886747
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|213596206|gb|DB960166.1|DB960166
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|209707880|gb|BW662086.1|BW662086
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGCAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|213604254|gb|DB978182.1|DB978182
EST:     GCAAGCGCCGATACCCTCAATCGT-TAGAGAGGAGAAGTTTGTGTG                         ATACGCACTATCATGATTGACAATATTGAGAAAATAATGGAGAGAGATGAC
genomic: GCAAGCGCCGATACCCTCAATCGTGT-GAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|254321070|gb|GR827519.1|GR827519
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|5057629|gb|AI736105.1|AI736105
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGA-AGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|16348943|gb|BI974538.1|BI974538
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|9983078|gb|BE657186.1|BE657186
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|24136750|gb|BU927260.1|BU927260
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|7286109|gb|AW598596.1|AW598596
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|192321054|gb|FK013528.1|FK013528
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|192321053|gb|FK013527.1|FK013527
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|11413060|gb|BF425080.1|BF425080
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|57575163|gb|CX548138.1|CX548138
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|15662923|gb|BI700286.1|BI700286
EST:     GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGGAGAGAGG
genomic: GTAATGCAAGCGCCGATACCCTCAATCGTGTGAGAGGAGAAGTTGGCGAGgcaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGG-AGAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccttcacttagtttcacacggtgacattagaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAGACAGCAACAATGCAAGACAGTGCAT
                                   ctttcatttctatc  CT-rich tract
                                    tttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttactctattgatgtttcacatcttgtgtcttcgtcgatttaagtcccttcacttagtttcacacggtgacattagaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAGACAGCAACAATGCAAGACAGTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -tgatgtt
- - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcacac