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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggattgataaatttctctttgatttcaactgtcctaaaaactttaggaactcttttaatgtcatttcaatcattcttatgtttggtctggtatctggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTATGCACTGAATCAACTTTCCATGTTTCTGGGGTTGATTGCTGCTGAGATAT

Basic information

species Glycine max
transcript GLYMA04G40760.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G49390.2 (Arabidopsis thaliana), 3'ss of exon 10
gttggattgataaatttctctttgatttcaactgtcctaaaaactttaggaactcttttaatgtcatttcaatcattcttatgtttggtctggtatctggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTATGCACTGAATCAACTTTCCATGTTTCTGGGGTTG-ATTGCTGCTGAGATAT
   || |  | | || |    |   |||      | |||  | |||||    ||     ||  |   |||| ||||  || ||||  |  |  | | |    || ||||||||||||||||||||||||||  |  | | |  ||| ||  ||    |  | |||| |      |   | |  |    ||  || ||    |||| | 
---gggtctacatatgttaaatctctttagctattactattatctttat--tcttgggaaacatgtattcattcatctttgtgtt--gatttatctgtttcttgaagGGTAAGTCCATCGAAGACACCAGTAAGGCCGCATTTTCCCCGCGCTGAGTTCAAGTGAAACTCTAGCCGGAGATCTTAAAATTATATAGCAAACGAGAGA-
















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|51335860|gb|CO979726.1|CO979726
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|208207004|gb|GE006701.1|GE006701
EST:     CTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: CTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|10238752|gb|BE807640.1|BE807640
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTNTGGGTTCACTGCCCATAAG                         GTATGCAGGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagG---G-----TAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGT
EST: gi|12773859|gb|BG238786.1|BG238786
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|254327105|gb|GR836714.1|GR836714
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|209727239|gb|BW663300.1|BW663300
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|254339083|gb|GR847800.1|GR847800
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|254334793|gb|GR844578.1|GR844578
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|10233834|gb|BE802722.1|BE802722
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAC                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|26268235|gb|CA819298.1|CA819298
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
EST: gi|192307294|gb|FK002372.1|FK002372
EST:     ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAG                         GGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT
genomic: ATTGCAGCTCTAAGCTGTAGTGGGGTGATTTTGGGTTCACTGCCCATAAGgttggattga ... tggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttttaatgtcatttcaatcattcttatgtttggtctggtatctggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTATGCACTGAATCAACTTTCCATGTTTCTGGGGTTGATTGCTGCTGAGATAT
   ttttaat  putative branch site (score: 3)
             atttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggattgataaatttctctttgatttcaactgtcctaaaaactttaggaactcttttaatgtcatttcaatcattcttatgtttggtctggtatctggtatgcagGGTAAGTCCATCGAAGACACCAGTTCGTTCACGTGCTCCTCGTCCTTCTATGCACTGAATCAACTTTCCATGTTTCTGGGGTTGATTGCTGCTGAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT