Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tacaacaagtaattctcttctccctcctcaattctattctattctattctattctatgcgagcaaataggagcaattagcgcttgaatttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAGCAGGTGTTTTCGGCAATGGAGGCGAACTACGAGGCGTGGGTCAACGGAT

Basic information

species Glycine max
transcript GLYMA17G35360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G35360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g09140.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------tacaacaagtaattctcttctccctcctcaattctattctattctattctatt--ctatgcgagcaaataggagcaa-ttagcgcttgaattt-----ctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAGCAGGTGTTTTCGGCAATGGAGGCGAACTACGAGGCGTGGGTCAACGGAT
| | || | | | || | || | ||||| | | | ||| | | |||| || ||| || || | ||||| ||||||||||| |||||| | ||||||||||||||||| ||| | || ||||||||| | || || |||||||||||||| |||||||| || |||||| ||||
gtaatcgaaagaaagaaaaaggaaaacccaaaaaaattgggtgtgatgaattcatttgcgaatacacgtggggggttttttttttttttttttcttctaattttcttgctaaccaaacaaaaagacccaaatttgctccgaaatttgtgcactcagATTCCTAAACGACCACGACTACCACGGGGGATTCGAGGAAGGTGAAATCGAGAAAGTATTCTCGGCAATGGAGGCCAACTACGACGCCTGGGTCCACGGC-
















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|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|26047534|gb|CA784292.1|CA784292
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|213607093|gb|DB957069.1|DB957069
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGA                         TTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
EST: gi|7147384|gb|AW509306.1|AW509306
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGA                         TTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|13790117|gb|BG652708.1|BG652708
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         T
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcaga-
EST: gi|20075392|gb|BQ094175.1|BQ094175
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         TACAACAAATTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaT--------T-CCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
EST: gi|18690813|gb|BM519661.1|BM519661
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         TACAACAAATTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaT--------T-CCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
EST: gi|208215789|gb|GE009775.1|GE009775
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGA                         TTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
EST: gi|213596654|gb|DB956046.1|DB956046
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         TACAACAAATTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaT--------T-CCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
EST: gi|209705615|gb|BW673584.1|BW673584
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         TACAACAAATTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaT--------T-CCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
EST: gi|213587068|gb|DB961763.1|DB961763
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGG                         TACAACAAATTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaT--------T-CCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGA
EST: gi|213592146|gb|DB965965.1|DB965965
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGA                         TTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
EST: gi|5761228|gb|AI966591.1|AI966591
EST:     GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGA                         TTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG
genomic: GCCGCCCGGACCTCTTCTCCAAACTCATCCTCATCGGCGCCTCCCCTAGGtacaacaagt ... atttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattctattctatgcgagcaaataggagcaattagcgcttgaatttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAGCAGGTGTTTTCGGCAATGGAGGCGAACTACGAGGCGTGGGTCAACGGAT
                                              tttctc  CT-rich tract
 tattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaacaagtaattctcttctccctcctcaattctattctattctattctattctatgcgagcaaataggagcaattagcgcttgaatttctcagaTTCCTGAACGACAAGGACTACCACGGGGGATTTGAGCAGGGAGAAATCGAGCAGGTGTTTTCGGCAATGGAGGCGAACTACGAGGCGTGGGTCAACGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG