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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgctcaaaaatcactagattatttatgcaaattttcttagttgaagtaaatttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAGTTAAGCTGTT

Basic information

species Glycine max
transcript GLYMA18G49340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G69620.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgttgctcaaaaatcactagattatttatgcaaattttcttagttgaag-taaat-ttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAG--TTAAGCTGTT
||  ||| ||  |     | |   |  ||  |       ||  ||    |||  |||| ||||  | | |       || || || || ||||| || |||||||| || |||||||| |||||||| ||||| |||||| | ||||||||||| ||||||   ||  | ||| |   ||  |    
gttcgtt-cttgagttcaattttgtatttgctttgtgcctttgtaaccaaagacaaatcttaatggttgttcttgtgtgttacagAATCATTCGTGCCTTCCTTGTGGAGGAGCAAAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCAAAGGAAAAGGTTGCTCCCAAGTGATCTAGACCC--

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttgctcaaaaatcactagattatttatgcaaattttcttagttgaagtaaatttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAGTTAAGCTGTT
         | ||  ||  | || ||||||        |||||||  || | ||  |         ||  |    |  |  ||||| ||||| |||||| | || || |||||||| |||||||||||||| |||||||||||||||||||| |||||||| || |||||||||| |    | 
--------gtaaatgatttcaagtttatttcg------tttcttaactgcactagttggggttttgattaataactttttcagGATAATTCGAGCTTTCTTGGTGGAGGAGCAAAAGATTGTGAAAAAGGTGTTGAAGATCCAGAAGGCAAAGGAAAAGCAAGCCTCAAAGAGTTGAAAAATG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S39_344V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------gtatgttgctcaaaaatc-actagattatttatgcaaattttcttagttgaagt---aaatttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAGTTAAGCTGTT
                | | ||  | | |  ||   |   ||     |       | ||| | | | ||     ||||   | | | ||||  ||  |  || || ||||||||||||||||| || ||||| || |||||||| || ||| |||||||||||||| |||| || ||   |||  | || | | |  ||   
attagtcattgtctgatttctttttaacagttctgttgtgttggccttctgggcatgcttggatcatgttttgcatttctgaaccaagtaaattt--tgcagCATCATTCGCGCTTTCCTTGTCGAGGAGCAGAAGATTGTGAAGAAAGTACTGAAGATCCAGAAGTCAAAGGAGAAATTGGCTGCTAAAACTCAGTCTTAA

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|193570861|gb|FK529936.1|FK529936
EST:     GGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|298192810|gb|HO033244.1|HO033244
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GGTTATTCGCGCTTTCCTTGTTGA
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGA
EST: gi|208327634|gb|GE125810.1|GE125810
EST:     CCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGC
genomic: CCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGC
EST: gi|193518530|gb|FK475709.1|FK475709
EST:     GGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGC
genomic: GGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGC
EST: gi|192310364|gb|FK002244.1|FK002244
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|151398936|gb|EV268807.1|EV268807
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|193484407|gb|FK450231.1|FK450231
EST:     CGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAG
genomic: CGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAG
EST: gi|163920689|gb|EH039970.1|EH039970
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|33388818|gb|CA852025.1|CA852025
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192310365|gb|FK002245.1|FK002245
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|7284738|gb|AW597288.1|AW597288
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|58024564|gb|CX711305.1|CX711305
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|58014987|gb|CX701729.1|CX701729
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192313246|gb|FK003366.1|FK003366
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|24205811|gb|BU965064.1|BU965064
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|5753167|gb|AI960454.1|AI960454
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|193304553|gb|FK273158.1|FK273158
EST:     CGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: CGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|7589597|gb|AW705368.1|AW705368
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|57575671|gb|CX548646.1|CX548646
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|193483394|gb|FK451461.1|FK451461
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGT
EST: gi|7590502|gb|AW706253.1|AW706253
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|15662700|gb|BI700071.1|BI700071
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|6072282|gb|AW101669.1|AW101669
EST:     GTAAACCGAGCCTATGGAGGTGTTATATCCGGGGGAGCTGTTAGAGAGAG                         GATTATTCGCGCTTTCCTTGTTGAA
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAA
EST: gi|58024472|gb|CX711213.1|CX711213
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
EST: gi|192320359|gb|FK013449.1|FK013449
EST:     GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAG                         GATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT
genomic: GTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgct ... cttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcaaattttcttagttgaagtaaatttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAGTTAAGCTGTT
                           atttaac  putative branch site (score: 3)
                                            tcttgct  putative PPT
      aaattttcttagttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgctcaaaaatcactagattatttatgcaaattttcttagttgaagtaaatttaacagctatgtaatcttgctatagGATTATTCGCGCTTTCCTTGTTGAAGAGCAAAAAATTGTGAAAAAGGTATTGAAGATCCAGAAGGCAAAAGAAAAGCAGGCATCAAAGAGTTAAGCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT