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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagatctctcttctcagtttccgattttcctttttacttcgctttcaaccccctccttttcaatttccccaatcttttgaaatctttcttcgaaccctaaaaacatctgtccccgattttcgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG

Basic information

species Glycine max
transcript GLYMA14G17930.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G080930_T02 (Zea mays), 3'ss of exon 1
gttcagatctctcttctcagtttccgattttcctttttacttcgctttcaaccccctccttttcaatttccccaatcttttgaaatctttcttcgaaccctaaaaacatctgtccccga---ttttcgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAA-------GATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG
                                                                                    |   | ||| | ||   ||||   | |||         |||| | |     ||||  ||| |    ||| |||| | |  ||||  ||   ||        ||| | ||         ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| |   
------------------------------------------------------------------------------------aatatcctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtac-taatttgaattaactctatttgtttctcttgtgacaagTTCAGGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCT---

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 1
gttcagatctctcttctcagtttccgattttcctttttacttcgctttcaaccccctccttttcaatttccccaatcttttgaaatctttcttcgaaccctaaaaacatctgtccccga---ttttcgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAA-------GATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG--
                                                                                          ||| | ||   ||||   | |||         |||| | |     ||||  ||| |    ||| |||| | |  ||||  ||   ||        ||| | ||         ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| | ||  
-----------------------------------------------------------------------------------------cctttggacatgaaaattgtttgtaatgtggtcttttggctgattgtttgggagtac-taatttgaattaactctatttgtttctcttgtgacaagttcagGAATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAA
















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|298170870|gb|HO015846.1|HO015846
EST:     GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|213589771|gb|DB969592.1|DB969592
EST:     CGCTCACTCTCTAGGGTTTTTATTTCTCTCTTCTCTCTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|13790205|gb|BG652796.1|BG652796
EST:     CTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|192324562|gb|FK016453.1|FK016453
EST:     CTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298179401|gb|HO027872.1|HO027872
EST:     CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|151395696|gb|EV265573.1|EV265573
EST:     CTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|208108759|gb|GD907163.1|GD907163
EST:     GCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGC
genomic: GCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGC
EST: gi|298185492|gb|HO030705.1|HO030705
EST:     CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|207702915|gb|GD686149.1|GD686149
EST:     GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|192299813|gb|FG993333.1|FG993333
EST:     TTTTTATTTCTCTCTTCTCTCTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: TTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|192295485|gb|FG987099.1|FG987099
EST:     CTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|8669525|gb|BE190632.1|BE190632
EST:     TCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: TCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|209700148|gb|BW652992.1|BW652992
EST:     CTCTCTAGGGTTTTTATTTCTCTCTTCTCTCTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298198145|gb|HO039684.1|HO039684
EST:     GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298164978|gb|HO011027.1|HO011027
EST:     GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|6070422|gb|AW099809.1|AW099809
EST:     CTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|192300160|gb|FG989282.1|FG989282
EST:     CTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298178379|gb|HO024114.1|HO024114
EST:     GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: GCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|7591104|gb|AW706844.1|AW706844
EST:     TTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: TTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298179203|gb|HO027674.1|HO027674
EST:     CTCTCTAGGGTTTTTATTTCTCTCTTCTCTCTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
EST: gi|298165150|gb|HO011199.1|HO011199
EST:     CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAG                         GTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG
genomic: CGCTCGCTCTCTAGGGTTTTTCTTTTTCTCTTCTCACTGCATCGCTTCAGgttcagatct ... taattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG
                                          tcttaat  putative branch site (score: 3)
                                       ttttcttaattttc  CT-rich tract
                 ttcaccgtttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagatctctcttctcagtttccgattttcctttttacttcgctttcaaccccctccttttcaatttccccaatcttttgaaatctttcttcgaaccctaaaaacatctgtccccgattttcgtttcccctttgcaagttcaccgtttaaatttaattaattttcttaattttcagGTTCTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA