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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctatctattgatgtttcacatcatgtgtctttgtctatttaagtcccttcacttagtttcacacgatgatattggaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGACAGTGCAT

Basic information

species Glycine max
transcript GLYMA12G09680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09680.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------actctatctattgatgtttcac-----atcatgtgtctttgtct-atttaagtcccttcac-ttagtttcacacga----tgatattggaactttcatttctat---------catacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGACAGTGCAT
                                                | |  |    ||||  ||| |      || | |  |  ||| || |   | |   ||| |  |  || |     ||    |||  || |   | |||||  | |           ||||||| ||  |  ||||||| || || |||||||| ||| |||| ||||||||  |||||||||||||||||||||||||||||||||||||||| ||  | |
gtataattgtttcttcgtatgatctctagatattactcagctatatccattgaaaaggttgaatttttatgagttattacgccttcttggctcacacaggcttctttaaatctgtcttgggtgaaagatgaagtttgttatctcattgttgtgttatcgtgtttacagATTCGATCGGTCATGGTAGAGAACATTGAGAAGATAATGGAAAGAGGTGATAGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGATAGCTCGT

upper sequence: GLYMA12G09680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------------------------------------actctatctattgatgtttcacatcatgtgtctttgtctatttaagtcccttcacttagtttcacacgatgatattggaactttcattt----ctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGACAGTGCAT
                                                                                            |||   |  ||| || ||  |  |  |   | ||  | |  ||||  |     | ||   |   || |||| | |    ||    | |      |  ||| ||||||||||| |||||||| || || |||||||| ||| |||||||||||||  ||||||| ||||||||||| ||||| |||||||||||||||||| | |
gcaagtatcattttgtcattgtgggggtttgtgcatgatttatgtgtatatgtgcaggagatgacctaatgcaacacttgtgtacatttctcacttgttacatt-atcttgaagtttgttctttttctttttgttaatacttaatatttttatggccatgatgttgtgctgacgacaactaaaaattgacattcagATACGCACCATCATGGTAGAAAACATTGAGAAGATACTGGAGAGAGGTGATAGGATTGAACTTCTTGTTGACAAAACTGCAACAATGCAAGACAGTTCTT
















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|208258648|gb|GE056383.1|GE056383
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|58019488|gb|CX706230.1|CX706230
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|298191166|gb|HO038645.1|HO038645
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGGGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|19270002|gb|BM886258.1|BM886258
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|16996834|gb|BM086206.1|BM086206
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|20811964|gb|BQ296442.1|BQ296442
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|22523664|gb|BU082475.1|BU082475
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|58016376|gb|CX703118.1|CX703118
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|16106385|gb|BI894125.1|BI894125
EST:     GCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|5607011|gb|AI901109.1|AI901109
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGCGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGACAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|193359955|gb|FK327161.1|FK327161
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|16348428|gb|BI974023.1|BI974023
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|308098861|gb|HO760702.1|HO760702
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|213598752|gb|DB964290.1|DB964290
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
EST: gi|15813797|gb|BI786072.1|BI786072
EST:     GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAG                         ATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC
genomic: GTAATACGAGTGCCGATACCCTCAATCGTGTGAGGGGAGAAGTTGGTGAGgtaagtacat ... tatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccttcacttagtttcacacgatgatattggaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGACAGTGCAT
                                   ctttcatttctatc  CT-rich tract
                       atgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctatctattgatgtttcacatcatgtgtctttgtctatttaagtcccttcacttagtttcacacgatgatattggaactttcatttctatcatacagATACGCACTATCATGGTGGACAATATTGAGAAAATATTGGAGAGAGGTGACCGGATTGAGCTTCTTGTTGATAAAACAGCAACAATGCAAGACAGTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -tgatgtt
- - - - - - - - - -cacatca
- - - - - - - - - - - - - - -gtctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcacac