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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatagtgacattgcttccttgtcactacctcttttttttttattccctcatcctccttatagataaggcttttattattttccttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA

Basic information

species Glycine max
transcript GLYMA09G30650.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30650.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G170400_T01 (Zea mays), 3'ss of exon 4
-----agaaatagtgacattgcttccttgtcactacctcttttttttttattccctcatcctccttatagataaggcttttattattttccttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA
     |||||     | |    ||  ||   |  |    ||  |  || |  ||    |  || |||  | ||||  ||| | | ||  |    ||| |    ||||  | ||  | |  |  |  ||| | ||||||||||| || || ||  || | ||||| |||||||||||||| |||||||||||||||||||| || |
atactagaaagctctaaacaattttttttggaaaaaaaattaatacttaaaacctcgcttttcattactg-taagtttttaactgttaactcatattat----agGTCCAAAAGCTTGTGGGGAAAATGGTAAAATGGTTAAAGGTCGGAGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGA

upper sequence: GLYMA09G30650.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G170400_T03 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------------agaaatagtgacattgcttccttgtcactacctcttttttttttattccctcatcctccttatagataaggcttttattattttccttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA
                                                                                                      |||||     | |    ||  ||   |  |    ||  |  || |  ||    |  || |||  | ||||  ||| | | ||  |    ||| |    ||||  | ||  | |  |  |  ||| | ||||||||||| || || ||  || | ||||| |||||||||||||| |||||||||||||||||||| || |
gtgcgctatgaccactcttttcagaagaagtgtagaatatttacatgcatcaatcgattccatctttcatctgatctcacttcaataaacaacacccatactagaaagctctaaacaattttttttggaaaaaaaattaatacttaaaacctcgcttttcattactg-taagtttttaactgttaactcatattat----agGTCCAAAAGCTTGTGGGGAAAATGGTAAAATGGTTAAAGGTCGGAGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGA

upper sequence: GLYMA09G30650.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G060886_T01 (Zea mays), 3'ss of exon 5
agaaatagtgacattgcttccttgtcactacctcttttttttttattccctcatcctccttatagataaggcttttatt------attttcc-----ttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA
           | ||  |||    | | |     ||  | ||  | |       |     ||||  | | | || |  |      |||||||     |||  ||| |  |||||||  |  ||| |   || ||| | |||||||| || |||||||| ||| | ||||| || ||||| || ||||| |||||||||||||| || || |
-----------ccttttttctaaatgagttaaaattggtgttcaaatgtactgactgaaatatatttgaagtttctggttcttgcattttccaacttttgtctctatgtagGTTGAACAGCTAGTTCAGAGAATGGTAAAATGGTTGAAGGTTGGTGGCTATATCTTCTTTAGGGAATCTTGCTTCCATCAATCTGGAGATTCAAAAAGGA

upper sequence: GLYMA09G30650.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 3
agaaatagtgacattgcttccttgtcactacctcttttttttttattccct---catcctccttatagataaggctt----ttattatttt---------ccttgattctttt---------cagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA
 | |||||  |   |  ||||  | || ||     |      | ||| | |   || |    ||  |||    | ||    |||||| ||           ||   |||||||         |||||||||||| | |||| ||||||| | |||||||| ||||||||||| | | | ||| | ||||| || | ||| || ||||| || ||||   | || |
-gtaatagcaatgctttttccagggcaataagatgtggaacatgattgcttgaacaacagttttgcagaattagtttacgtttattaattcagagctctgtctctgttcttttatggactagcagGTTGAGAATCTGGCTGAAAGGATGGTTAAATGGTTGAAAGTTGGTGGTTTTCTCTTCCTTAGAGAGTCTTCTTTTCATCAATCGGGTGATTTTCAAAGCA

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|193386941|gb|FK351238.1|FK351238
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATG-TTAAAAGTTGGTGG
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGG
EST: gi|193318467|gb|FK287543.1|FK287543
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAA
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAA
EST: gi|13311711|gb|BG405362.1|BG405362
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
EST: gi|208165796|gb|GD963728.1|GD963728
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGA
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGA
EST: gi|192310550|gb|FG999223.1|FG999223
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTCAAAAGTTGGTGGATAT
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
EST: gi|207816616|gb|GD787485.1|GD787485
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTACCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
EST: gi|207764672|gb|GD738039.1|GD738039
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
EST: gi|208269168|gb|GE068217.1|GE068217
EST:     TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGA
genomic: TTGATCTGATATTCTCAAATTGGTTACTCATGTATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGA
EST: gi|207691982|gb|GD673899.1|GD673899
EST:     ATCTTTCAGATAAAGAG                         GTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT
genomic: ATCTTTCAGATAAAGAGgtgagttttt ... ttcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctcatcctccttatagataaggcttttattattttccttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA
                                       ccttgat  putative branch site (score: 5)
                          cttttattattttcct  CT-rich tract
                           ttttattattttcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaatagtgacattgcttccttgtcactacctcttttttttttattccctcatcctccttatagataaggcttttattattttccttgattcttttcagGTTGAGAATTTAGCTGCAAGGATGATCAAATGGTTAAAAGTTGGTGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA