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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtttggagtaaggggcttttttatgaacatgctgagttttttttttctttttctttttttaatttttccatctttcctcactttctatactgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCT

Basic information

species Glycine max
transcript GLYMA18G39930.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G39930.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 5
tagtttggagtaaggggcttttttatgaacatgctgagttttttttttctttttctttttttaattttt------ccatctttcctcactttctata-ctgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCT
         |    | | ||||  |||||  |    | |||| | |   || ||    |  ||| || |      |||  |  | |    ||||||  | ||  ||||||||| ||||| ||||| | ||| || ||  | |||||| ||||||| || |||||||||||||||||  |||| ||||| || ||||| |||||   |
-------atgaggagtgattttaaatgaatttatcaatttttatctacattgtttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
















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|208333137|gb|GE127414.1|GE127414
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGAACAAAGATGGAGGT
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGA-CAAAGATGGAGGT
EST: gi|151397652|gb|EV267525.1|EV267525
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|208106222|gb|GD905149.1|GD905149
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|58019388|gb|CX706130.1|CX706130
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|214006979|gb|DB988430.1|DB988430
EST:     GGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGGCTTCGGGAACTACTTGTAGG
genomic: GGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|208098334|gb|GD894755.1|GD894755
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAGG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|7028397|gb|AW458180.1|AW458180
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGACGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|208194340|gb|GD987623.1|GD987623
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|193443566|gb|FK409256.1|FK409256
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|213620500|gb|DB957344.1|DB957344
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACNATTATAAG                         GGCTGGTGGCTTGCAA
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAA
EST: gi|208279633|gb|GE081260.1|GE081260
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|208252188|gb|GE046592.1|GE046592
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|58022869|gb|CX709610.1|CX709610
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|193581596|gb|FK538299.1|FK538299
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|58016336|gb|CX703078.1|CX703078
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|208110158|gb|GD907246.1|GD907246
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAG
EST: gi|207711258|gb|GD694715.1|GD694715
EST:     CCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: CCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|8825861|gb|BE209591.1|BE209591
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|58019799|gb|CX706541.1|CX706541
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGG
EST: gi|192327079|gb|FK015471.1|FK015471
EST:     AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAG                         GGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTAC
genomic: AAGGCTGAGCAATATCTGGCTGATTCCGGCATCCCATATACAATTATAAGgtacatcaac ... actgagccagGG-CTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttctttttttaatttttccatctttcctcactttctatactgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCT
                               tcctcac  putative branch site (score: 2)
                   tttttccatctttcct  CT-rich tract
     ttttctttttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtttggagtaaggggcttttttatgaacatgctgagttttttttttctttttctttttttaatttttccatctttcctcactttctatactgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - acatgct