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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatccattgcctacaccaagaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaattatagctgtttatttacctggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 10
aatccattgcctacaccaa-gaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaattatagctgtttatttacctggtt-atacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
              |  || |   || |  |||   |  | |   |     | |  ||||  |    | ||||||  ||| || ||| |  | ||  | |||||||  ||| || ||||||||||||  ||||| ||||||||||||||||| |
------------gtatgaatggggtttatttgccgattctgtgtctcagctttactttgtggc----caaattat--ctgattgtttgctggatttgtccagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 9
aatccattgcctacaccaa-gaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaattatagctgtttatttacctggtt-atacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
              |  || |   || |  |||   |  | |   ||    | |  ||||  |    | ||||||  ||| || ||| |  | ||  | |||||||  ||| || ||||||||||||  ||||| ||||||||||||||||| |
------------gtatgaatggggtttatttgccgattctgtc--ttagctttactttgtggc----caaattat--ctgattgtttgctggatttgtccagGCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 10
aatccattgcctacaccaagaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaatta--tagctgtttatttacctggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
              || |       | | |  ||||  | |  ||||      || | ||| ||     |  |  ||  || | | || | |  || | |||||||  ||| || ||||||||||||  ||||| ||||||||||||||||| |
------------gtacgagtggggcctatt--ttgttgtttcctttgtgtctctgctttactttgtggcacaaattatttgctcactttctt--ttgtgcagGCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G427620_T01 (Zea mays), 3'ss of exon 5
aatccattgcctacaccaagaaattca-aatgcttgtcttcttatttgcagtcatgttgtacctt-tcctaattatagctgtttatttacctggtt-atacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
      || | ||      |  ||  |    | || | | |  |||     ||| | | ||| || |    | |||| ||| || ||| |  | ||  | |||||||  ||| || ||||||||||||  ||||| |||||||||||||||||  
--cttcttccatatgttctggtatgaatggggtttatttgccgattctgtctca-gctttactttgtggccaatatatctgattgtttgctggatttgtccagGCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACA

upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 11
aatccattgcctacaccaagaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaat-tatagctgtttatttacctggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
 ||   ||   | |        | |||     || |||| | ||||  | |  | || |   |||     | |||  |||||  |||  ||    | |||||| |||||| |||||||||||| |||||| || ||||||||||| || ||||
gatttgttagat-cttagcttcactcattatgttttcttgtaatttttattttttttcttggtttaaaggtgtatgtctgttgttttgtctataaaaacagGCAAGGTTTCTTGAAGCTGCTGCTGCATATAAGAAGAAGATTGGGTTTAATG

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|207703122|gb|GD684900.1|GD684900
EST:     GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
genomic: GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
EST: gi|163926470|gb|EH039217.1|EH039217
EST:     GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAA
genomic: GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAA
EST: gi|5760217|gb|AI965580.1|AI965580
EST:     TGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
genomic: TGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
EST: gi|193624477|gb|FK574329.1|FK574329
EST:     CTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCNGGGTTTTTTGAAGCTGCTGTTGCAT-CAAAAAGAAGATTGGATTCAAT
genomic: CTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
EST: gi|207762590|gb|GD733437.1|GD733437
EST:     ATATGGAGCGAGAGCTTAATCATTTG                         GC-AGGTTTTTTGAAGCTGCNGTTGCATACAAAAAGAAGATTGGATTCAAT
genomic: ATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
EST: gi|208234523|gb|GE030472.1|GE030472
EST:     GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTT
genomic: GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTT
EST: gi|16276935|gb|BI942118.1|BI942118
EST:     GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
genomic: GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
EST: gi|13478586|gb|BG508003.1|BG508003
EST:     GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTG                         GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT
genomic: GTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATTTGgtgcgtgaat ... ggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtcatgttgtacctttcctaattatagctgtttatttacctggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG
                   tcctaat  putative branch site (score: 2)
                                tgtttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatccattgcctacaccaagaaattcaaatgcttgtcttcttatttgcagtcatgttgtacctttcctaattatagctgtttatttacctggttatacagGCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- -ccattgc
- - - - - ctacacc
- - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - -tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttt