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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatcctttaccattatgcttgtattgcatacttttattttctgcttatcatggctgttccatatttccgattctgatattactttatctgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT

Basic information

species Glycine max
transcript GLYMA04G37120.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 6
---------actatcctttaccattatgcttgtattgcatac--ttttattttctgcttatcatggctgttccatatttccgattctgatattactttatctgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
          |||| ||| |   |||| ||  || |  || |  |  || | | ||||  | ||||   ||  ||| |||   |||| | || |  | || | |||   |||||||||||| || |||||||| || || |||||  ||||||||||| | || |||||||| || || |||||||| || | ||| ||||||||  || |
gtatgtgactctattcttcaattttattctgctaataaatccagtactaatatgtgctc-ttatgg---tttaatagttcattttctaacataaaatcatttttgc---agCCAAACTTGTACCAGTTGGATATGGCATCAAGAAGTTGCAAATTATGATGACCATTGTGGACGATCTTGTTTCTGTGGACAGTCTCATTGAGGATTATTT

upper sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 6
--------actatcctttaccattat-gcttgtattgcatacttttattttctgcttatcatggctgttccatatttccgattctgatattactttatctgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
         || |  || ||  ||||  || |||  ||| || |      |     ||  ||   | |||   |      | ||| || ||| ||  | |||    ||||||||||||| || |||||||| ||||| |||||| |||| ||||||||||| |||||||| ||| | |||||||| ||    ||||||||||||||  |
ttttgtgccctgtttttaacttttattactcgtaaggcaaacatcggagattaaagtaatat---tattctggaac----aatctaattttaattgttttgt--tgcagCCAAACTTGTACCAGTTGGATATGGTATAAAGAAATTGCAGATTATGCTTACCATTGTGGACGACTTGGTTTCTGTGGACGACCTTATTGAGGAACAGTT
















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|192309529|gb|FK000191.1|FK000191
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTCGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|58017474|gb|CX704216.1|CX704216
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|151401263|gb|EV271077.1|EV271077
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGA
EST: gi|9258998|gb|BE347145.1|BE347145
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTTGGGTGCAT----                         CCAAACTTGTTCCTGGTGGGATCCG-TATTAAGAA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGG-ATACGGTATTAAGAA
EST: gi|19346370|gb|BM891250.1|BM891250
EST:     GTGAGATCTGTTCAGATGGAA-GGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|31307073|gb|CD392276.1|CD392276
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|31462978|gb|CD405006.1|CD405006
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCCAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCCAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|8401588|gb|BE057152.1|BE057152
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|192329979|gb|FK021565.1|FK021565
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|22523638|gb|BU082449.1|BU082449
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|151396767|gb|EV266640.1|EV266640
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTCGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|58015143|gb|CX701885.1|CX701885
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|31561132|gb|CD486970.1|CD486970
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGT
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGT
EST: gi|192329978|gb|FK021564.1|FK021564
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|254318263|gb|GR832431.1|GR832431
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|254314708|gb|GR829701.1|GR829701
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAA-CTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|4436972|gb|AI522837.1|AI522837
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|192300142|gb|FG989264.1|FG989264
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|254314709|gb|GR829702.1|GR829702
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|193635492|gb|FK584831.1|FK584831
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|6964003|gb|AW432696.1|AW432696
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|6848971|gb|AW351261.1|AW351261
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|15813987|gb|BI786262.1|BI786262
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|192295190|gb|FG986909.1|FG986909
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGG-G--TGCAT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|26058029|gb|CA800943.1|CA800943
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|42722502|gb|CK768401.1|CK768401
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|4286063|gb|AI440993.1|AI440993
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTTGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|254318262|gb|GR832430.1|GR832430
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGGTATTAAGAAACTGCAAATTATGCTT
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGG-TATTAAGAAACTGCAAATTATGCTT
EST: gi|151396946|gb|EV266819.1|EV266819
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|9564337|gb|BE473846.1|BE473846
EST:     GAATCAGTGAGATCTGGTCAGATGGAAGGGGTGCTTTGGCGTGCAT-T--                         CCAA-CTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|151409150|gb|EV278958.1|EV278958
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|31463360|gb|CD405388.1|CD405388
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|151402916|gb|EV272729.1|EV272729
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|11687926|gb|BF595602.1|BF595602
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCAT----                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
EST: gi|7692495|gb|AW760600.1|AW760600
EST:     GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGC----AT                         CCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA
genomic: GAATCAGTGAGATCTGTTCAGATGGAAGGGTTGCTTTGGGGTGCATGTATgttattttta ... tgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatcatggctgttccatatttccgattctgatattactttatctgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT
                           ttctgat  putative branch site (score: 3)
                                      ctttatct  putative PPT
                              tgatattactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatcctttaccattatgcttgtattgcatacttttattttctgcttatcatggctgttccatatttccgattctgatattactttatctgtgccccagCCAAACTTGTTCCTGTTGGATACGGTATTAAGAAACTGCAAATTATGCTTACTATTGTGGATGACCTAGTTTCTGTTGATACTCTTATTGAGGAACATCT

- - - - - - - - -tgcttgt
- - - - - - - - - - - - - -gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - catggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg