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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcactattctatccatcattatgaaagaatttggatcttatgatacataactgttgagtattgactaaaattatcttgcatgtatgttgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAGCAGATGAGAAGAAGGCATGGCTGATATTGGCTTGGGCCAGCACCATATC

Basic information

species Glycine max
transcript GLYMA10G37710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G37710.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g00780.t01 (Vitis vinifera), 3'ss of exon 2
tctgcactattctatccatcattatgaaagaatttggatcttat--gatacataactgttgagtattgactaaaattatcttgcatgtatgttgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAGCAGATGAGAAGAAGGCATGGCTGATATTGGCTTGGGCCAGCACCATATC
|    | ||   | |  ||||   |   | ||  ||    |||   ||  ||    |  | |    |  ||    || |  |   | | | |  | ||  ||||||||||||||||| | |||| ||||| ||||| |||  |||||||  ||| || |||||||||||||||||||| || ||||||| ||||||  |  |
ttcctaatagaatctttatcaaagtctgataagatgaccattactggaaccacgcataatcaaggcttccttctttttttctttttttgtatgatgat--agTTCTCTTGCTTGGAGCACGGGTGGCAGCATCAGCAGCTCAAATTTCCGCAGCCGAAGAGAAGAAGGCATGGCTGATCTTAGCTTGGGTCAGCACTGTGGC
















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|214007843|gb|DB987787.1|DB987787
EST:     GCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAAAT-TCCCAACAG                         TTCTCTTGCTTGGAGGAATTGTAGCAGATTCAGCTGCTGCAATTTCCAAAG
genomic: GCAATTGTCATACTTGTCCTATCAAATTTGGCTTC-AAATGTACCAACAGgtaagtagac ... tgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
EST: gi|9566042|gb|BE475613.1|BE475613
EST:     TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAG                         TTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
genomic: TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAGgtaagtagac ... tgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
EST: gi|23733515|gb|BU764956.1|BU764956
EST:     TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAG                         TTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
genomic: TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAGgtaagtagac ... tgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
EST: gi|4397050|gb|AI496047.1|AI496047
EST:     TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAG                         TTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
genomic: TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAGgtaagtagac ... tgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
EST: gi|6848242|gb|AW350532.1|AW350532
EST:     TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAG                         TTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG
genomic: TGCAATTGTCATACTTGTCCTATCAAATTTGGCTTCAAATGTACCAACAGgtaagtagac ... tgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacataactgttgagtattgactaaaattatcttgcatgtatgttgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAGCAGATGAGAAGAAGGCATGGCTGATATTGGCTTGGGCCAGCACCATATC
                    gactaaa  putative branch site (score: 2)
                tattgactaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcactattctatccatcattatgaaagaatttggatcttatgatacataactgttgagtattgactaaaattatcttgcatgtatgttgttatctagTTCTCTTGCTTGGAGGAAGGGTAGCAGCCTCAGCTGCTGCAATTTCCAAAGCAGATGAGAAGAAGGCATGGCTGATATTGGCTTGGGCCAGCACCATATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- tgcacta
- - - - - - - -ccatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgta