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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggattgtattctcggttgagttaatttgacaatcatttggcatttatgggcatcctagtttgtatttgtataggcttctaactttttgttgttcaatttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTTCCAGCGTACAGAGCCCCTGCAAGATCTTGATCGAATTTTGTCAAAG

Basic information

species Glycine max
transcript GLYMA04G41530.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------gtggattgtattctcggttgagt--taattt-gac----aatcatttggcatttatgggcatcctag------tttgtatt-tgtataggcttctaactttttgttgttcaatttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTTCCAGCGTACAGAGCCCCTGCAAGATCTTGATCGAATTTTGTCAAAG
                           || | | | ||      | | |  |||||| |||      |  |||     || ||||  ||||        |||  ||| | | |    |||  | || |     ||   ||||| |||||| ||  | || ||||| | ||||||  ||||||||||| |||| |||||| |||| ||||||||  |||||||||| ||| |||| ||  |||||
gtgaacttttttgccttcattttagaatgcaattttttaaaaaataattgataatttcgacttctggttgtttctgtcttttgggtctcctgcaaaagttttacattatattttaaattcccatttatgccctttttttttctgcagGCAATATAGGGAGTATTTAGAGAATCTACTGGAGTATCTGATATATTTTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG
















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|193346751|gb|FK312175.1|FK312175
EST:     GATGTTTTCTCAGACACGGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
EST: gi|193432544|gb|FK394272.1|FK394272
EST:     GATGTTTTCTCAGACACGGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATT-GGCGAATCTTTTGGAGTATCTGTTATA
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
EST: gi|193427334|gb|FK394830.1|FK394830
EST:     ATTGTTTTCTCAGACACGGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
genomic: AT-GTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
EST: gi|193492609|gb|FK455733.1|FK455733
EST:     GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
EST: gi|193362991|gb|FK328755.1|FK328755
EST:     GATGTTTTCTCAGACACGGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATA
EST: gi|209711675|gb|BW674038.1|BW674038
EST:     GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
EST: gi|193325953|gb|FK292254.1|FK292254
EST:     ATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCCGTTATACTTTTT
genomic: ATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
EST: gi|193426610|gb|FK391261.1|FK391261
EST:     GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
EST: gi|193354591|gb|FK319099.1|FK319099
EST:     GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTT
genomic: GATGTTTTCTCAGACACAGATAAGATTCCCCGCAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTT
EST: gi|193437266|gb|FK403035.1|FK403035
EST:     TGTTTTCTCAGACACGGATAAGATTCCCCGCAAAAATGAAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATTCTTTTGGAGTATCTGTTATA
genomic: TGTTTTCTCAGACACAGATAAGATTCCCCGCAAAA-TGAAAA-TGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAAT-CTTTTGGAGTATCTGTTATA
EST: gi|193564745|gb|FK517158.1|FK517158
EST:     CAGACACAGATAAGATTCCCCGCCAAAATGAAAATGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATAC-TTTT
genomic: CAGACACAGATAAGATTCCCCG-CAAAATGAAAATGACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTT
EST: gi|193725639|gb|FK660647.1|FK660647
EST:     TTTCTTCAGACACAGATAAGATTCCCCGCCAAAATAGAAAATAGACCAG                         GCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTT
genomic: TTTC-TCAGACACAGATAAGATTCCCCG-CAAAAT-GAAAAT-GACCAGgtggattgta ... atttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcctagtttgtatttgtataggcttctaactttttgttgttcaatttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTTCCAGCGTACAGAGCCCCTGCAAGATCTTGATCGAATTTTGTCAAAG
                         ttctaac  putative branch site (score: 1)
                                              tttcttc  putative PPT
        tttgtatttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggattgtattctcggttgagttaatttgacaatcatttggcatttatgggcatcctagtttgtatttgtataggcttctaactttttgttgttcaatttcttcagGCAGTACCGAGAATATTTGGCGAATCTTTTGGAGTATCTGTTATACTTTTTCCAGCGTACAGAGCCCCTGCAAGATCTTGATCGAATTTTGTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA