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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtgctgcttggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

Basic information

species Glycine max
transcript GLYMA14G36540.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 6
gtaagttgtgctgcttggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatat-attta--atttca-tgaattatgt---cctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                   |||  |     |||      || || |  | || |||| | ||||   |||||| |||||  |||    ||  || |||||||| |||||||||||||| || |||||||||||||| || || || ||||| || || || || |||
-----------------------------------gtatgctagcctttccttcccaattatattctctaaatttgatttgccatttcactgaatagtgtatttctgcagCTATGGTGAATCATTCCCTGTTTCTGCGGAAGTTCTTGATTCTAGCTTCTGTCTTCCGATTGGGAAGGCTAAG

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 8
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttgtgctgcttggttt-gttcatgaaaatgagtagt-catagattttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
|||||| ||  | ||   ||  |||| || |  ||| |||  | ||   | | | |||||| | |  || ||       || ||||||| |         |  ||||||||||| ||||||||| |||| |  ||||  |||||||| ||||| || ||||||||||| ||||| |||
gtaagtagtattcctaatttgagttcttgcatgtgattagagcctacggtctcatatcagtacctccttaaa-------ttgatttcatca---------tgcagATATGGTGAATCATTCCCTATTTCAGAAGAAGCCCTTGATTCAAGTTTCTGTCTTCCCATAGGCAAAGCCAAG

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttgtgctgcttggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
              || || | || |||     || |  ||    |||     |||| |   |  ||  |   ||  || | ||   |||||   | ||  ||||||||| |||| ||||||||||| |  |||| ||||||||||||||| | |||||| ||||| |||||||||
-------------gttagtgttttgatgcttgagatttctctgtaatt---ggatcattgtatactt--actcatccttgagtt---gaatttcatgctgcagATATGGTCAGTCTTTCCCTGTTTCAGAGGAAGCTCTTGATTCCAGTTTCTCCCTTCCAATAGGGAAAGCAAAG

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|20498733|gb|BQ273663.1|BQ273663
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|20498857|gb|BQ273787.1|BQ273787
EST:     GCTGCTATAAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|19053203|gb|BM731870.1|BM731870
EST:     CTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: CTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|9439950|gb|BE440462.1|BE440462
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|7588536|gb|AW704259.1|AW704259
EST:     GCTGCTATTANGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTC-AGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|254319588|gb|GR829100.1|GR829100
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|120533350|gb|EH261483.1|EH261483
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCNCTGTTTCGGNCGAAGT-CTTGATTCCGGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|192323797|gb|FK015608.1|FK015608
EST:     GCTGCTATCAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGT
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGT
EST: gi|37994649|gb|CF806308.1|CF806308
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|298169681|gb|HO021041.1|HO021041
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|151396530|gb|EV266407.1|EV266407
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|17962851|gb|BM269607.1|BM269607
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|5606648|gb|AI900746.1|AI900746
EST:     GCTGCTATTAGGGACCCTGATCCTGTT-TTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|254334369|gb|GR844154.1|GR844154
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|207714211|gb|GD694990.1|GD694990
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|207737078|gb|GD713125.1|GD713125
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTCTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|254340298|gb|GR858423.1|GR858423
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|254335254|gb|GR846751.1|GR846751
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|10845821|gb|BF068863.1|BF068863
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|151397384|gb|EV267257.1|EV267257
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
EST: gi|207835633|gb|GD805630.1|GD805630
EST:     GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTT                         ATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG
genomic: GCTGCTATTAGGGACCCTGATCCTGTTGTTTTCCTTGAAAATGAATTGTTgtaagttgtg ... tgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG
                                             tgtcctct  CT-rich tract
          ttcttgtttcaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtgctgcttggtttgttcatgaaaatgagtagtcatagattttgacatcagttcttgtttcaaaatatatttaatttcatgaattatgtcctctagATATGGTGAGTCATTCCCTGTTTCGGCCGAAGTTCTTGATTCCAGTTTTTGCCTTCCCATAGGAAAAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG