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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

Basic information

species Glycine max
transcript GLYMA16G05450.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
gtttgaggtctgtttcatttgcatcttataacttgatatata-aaaggtcctgatacctgataatatgacctgtataac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
   ||   |  |   || |    | || |   || || | ||  |  |   || |  |   | || |   || |  | | ||  ||   |||  || ||  |||| || |||||||||||||| || |||||||||||||| ||  ||||||| ||||||||  | ||    || |||  |||||||| |||     | ||| |
---tggcatg-gcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT

upper sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 3'ss of exon 3
---gtttgaggtctg-tttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
   | |||   | || | ||||  | |   |||      | |||       |  |  |||||    | || |    |||    ||| |||| | |      |||| ||||||||||||||||| || |||||||||||||| || |  ||||| ||||| ||  | ||    || |||   ||||| | ||||    | ||  |
tctggttgttttttggtatcataagaaatatatcttgccaaataccttctctatttctacctttagacattattattatttt-taataatgatatact---cagATACAATGATGAAGTTTGCATCCTTTGAGACCATTGTTGAACAAATCTACAAGCATGCTGTTCCTGTCCCGAAGTCAGAGTGTAGCAAATCATTCCAGTT

upper sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacct-gtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
  ||||     ||| | || |   | ||||   ||    |  ||    |  |   |  | ||||  ||| ||     | |       | |  | | | ||||| || ||||||||||||||||| ||||||||||| || ||||| ||||| ||||| ||  | ||    || |||  |||||||| |||       ||  |
aatttggtagttgtattatatat-ttttatctattctcgttcaagccatattctcatattataagctgaactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
  ||||     ||| | || |   | ||||   ||  | |  ||    |  |   |  | ||||  || ||      | |       | |  | | | ||||| || ||||||||||||||||| ||||||||||| || ||||| ||||| ||||| ||  | ||    || |||  |||||||| |||       ||  |
catttggtagttgtattatatat-ttttatctattcttgttcaagccatattctcatattataagctgtactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 3
--gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
   ||||   | ||| | || |  |  ||||   ||   ||  ||    |  |  ||  | ||||  || ||     |     |    | |  | | | ||||| || ||||||||||||||||| ||||||||||| || ||||| || || ||||||||  | ||    || |||  |||||||| |||       ||  |
taatttggtatttgtattatat--aatttatttattatcatgcaagccatattcttatgttataagctgtactcacctgttgcactcgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATATACAAGCACGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

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|9439983|gb|BE440494.1|BE440494
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|18038974|gb|BM307268.1|BM307268
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|208319383|gb|GE113376.1|GE113376
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|21993585|gb|BQ785113.1|BQ785113
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|7591542|gb|AW707273.1|AW707273
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|192324693|gb|FK018759.1|FK018759
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|19938613|gb|BQ081803.1|BQ081803
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|10237660|gb|BE806548.1|BE806548
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|23052981|gb|BU577472.1|BU577472
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|21888708|gb|BQ741921.1|BQ741921
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|13481245|gb|BG510588.1|BG510588
EST:     CTTAGGGCTGTACAAGGGATTAGTGCCTATATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: CTTAGGGCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|208023912|gb|GD822310.1|GD822310
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|7588312|gb|AW704110.1|AW704110
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|22526003|gb|BU084814.1|BU084814
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|208280818|gb|GE078818.1|GE078818
EST:     CTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: CTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|21600641|gb|BQ610972.1|BQ610972
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|23728600|gb|BU762362.1|BU762362
EST:     CTTAGGGCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: CTTAGGGCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
EST: gi|17022287|gb|BM093321.1|BM093321
EST:     GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCAT                         ACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA
genomic: GCTGTACAAGGGATTAGTGCCTCTATGGGGACGACAGATTCCATgtaagttagc ... tttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
                          gtataac  putative branch site (score: 3)
                                        tgttctttctt  putative PPT
                           tataacataaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA