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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGGATTATGAGACAAGAAACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttcttttacatttgctgtcatcattcacttgcttttcgctctttctcggttaaaacatttctttttatgtgcatgcttgcttattgatttttatt...

Basic information

species Glycine max
transcript GLYMA13G18950.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18950.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 6
GAAGGGATTATGAGACAAGAAACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttcttttacatttgctgtcatcattcacttgcttttcgctctttctcggttaaaacatttctt-----tttatgtgcatgcttgcttattgatttttatt---
||||||| |||||||||||||| || |||||||| |||||| || |||| ||||||||||| || || | |||| || |   | ||| |||| | |   |   |||  | |||   | ||    | | | |  |||  |     || ||     || |    |    |    ||||   
GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATATGGCTGAGCAGCTTGCTATGgtaggtccc--tgcatgtgctttaactgt---cttattattc---cgttgaatgctgagatgttttctggatgttgatacctttgttactcttgcaacccatattttg
















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|151400304|gb|EV270118.1|EV270118
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAA-G                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATCCAAGTTTCTTGTTTG
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|298181570|gb|HO025745.1|HO025745
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCA
EST: gi|192301726|gb|FG997640.1|FG997640
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAG
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAG
EST: gi|151398563|gb|EV268434.1|EV268434
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|151403355|gb|EV273165.1|EV273165
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|254347887|gb|GR854136.1|GR854136
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|213595497|gb|DB966551.1|DB966551
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCANAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|192312569|gb|FK005027.1|FK005027
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATT
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATT
EST: gi|213591304|gb|DB959874.1|DB959874
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|151397287|gb|EV267160.1|EV267160
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGATATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|48575725|gb|CO036542.1|CO036542
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|209709595|gb|BW661922.1|BW661922
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTG
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTG
EST: gi|209714364|gb|BW677064.1|BW677064
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCANAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGA
EST: gi|298174324|gb|HO017660.1|HO017660
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTAT
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTAT
EST: gi|192312568|gb|FK005026.1|FK005026
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
EST: gi|192300056|gb|FG991860.1|FG991860
EST:     ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG                         ATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA
genomic: ACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttctt ... tgagttgcagATTTCCAAAGAGCATGGTGGTATCCTGAGATTTATTCAAGTTTCTTGTTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGGATTATGAGACAAGAAACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAGgtatgttcttttacatttgctgtcatcattcacttgcttttcgctctttctcggttaaaacatttctttttatgtgcatgcttgcttattgatttttatt

- - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG