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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT

Basic information

species Glycine max
transcript GLYMA17G14450.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g18030.1 (Oryza sativa), 3'ss of exon 1
ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgc-agGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT
 |    ||||||   |    ||  ||  ||||   | |  |        | |  |||  |   |  || |  ||    |  |   | |   |  || | |||| || || |||||||||||||| |||||||| |||||   ||||||||||||||| ||| | |  || |||||||||||||
atggcgttcaagtttttta-tattgccagaaaataattttatagcaccttgcagcaaaaggggagaatgtgatacgcataaaattgttttgtaactcctagGTTCTTATCATGGACAAACTTACGGTGAAGATTATGTCATTTTCTTGCAAGATGGCAGATGTGATGGAAGAAGGTGTTTCAT

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 2
ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT
 | || ||   |||   ||  |||  ||    ||||||     |    ||  | || ||   |  ||  |   ||||  ||||||  | |        |||| || || ||||||||||||||||| |||||||||||   ||| ||||||||||| |||||||| || ||||| |||||||
gtattcttggcgaatggaggaagatgttct--tctagt-----ttcaaatgttccattttcatg-cacataaaattgtgtcatgaatttc--------agGTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
--ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgca-----gGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT
   | |||| |  | | |   ||   |  ||    | ||  ||  | ||    ||| ||  ||| ||   | | | | || | |  |  | |||    | |     |||||| || ||||||||||||||||| |||||||||||  |  | ||||| ||||||||||||||  | ||||| |||||||
gtatgttttccttgtacttcactgtggactgg---ccagataatgtttttccgctttaag-gttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT

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|209703154|gb|BW673313.1|BW673313
EST:     ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAG                         GTACTCATAATGG
genomic: ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAGgtataagatg ... ttgcctgcagGTACTCATAATGG
EST: gi|207830531|gb|GD802881.1|GD802881
EST:     ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAG                         GTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
genomic: ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAGgtataagatg ... ttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
EST: gi|10237389|gb|BE806277.1|BE806277
EST:     ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAG                         GTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
genomic: ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAGgtataagatg ... ttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
EST: gi|193730259|gb|FK667431.1|FK667431
EST:     ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAG                         GTACTCGTAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
genomic: ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAGgtataagatg ... ttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
EST: gi|213610646|gb|DB961121.1|DB961121
EST:     ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAG                         GTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG
genomic: ATGAAATGCTTAGGTCAGCGAAAACAGGAGATTCAAAATCTACATGGAAGgtataagatg ... ttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT
 tgttgat  putative branch site (score: 4)
                                            cttgcct  putative PPT
          aattgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttttcaagaaatcagctagagcttgaaatctagtaaaattgttgatacttcaattgtttatcatcttgtattggttcatgagctgcttgcctgcagGTACTCATAATGGACAAACTTACTGTGAAGATAATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGTGTTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - gagcttg
- - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagctgc