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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaagggggatttttgataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA

Basic information

species Glycine max
transcript GLYMA02G07250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------catt-aagggggatttttgataaactttttattatg---aagttttattttccattt--tactttg----------gttcattgttactttgtgtatt-----ttttccattgcttt----atagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
                                          ||||   | |||  | | ||   | ||  |   ||    ||  || |  || ||  |  ||||             ||| | ||     ||| |||||     || | | |  | ||    ||||||||| |||||||| ||||| |||||||| ||||||||||| || ||  | || |||||||||||||||||  | ||||||||| | |||||||| || |
gtttgagaatttcactcaccgacttatgctctttcttcagaccattcgtgtgggcatgtagacctatttactggcatataaaaacttcagctttcacctgctactaaaagagacagatgtttactgagtaattgagtattgactattgtacttaaccttctggatagGCTTACACATATTTAGACGAGGCACACAGTATTGGAGCTGTTGGTAAAACCGGGAGAGGTGTTTGTGAGCTACTAGGTGTGGATCCAGCTGATGTCGATA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g70360.1 (Oryza sativa), 3'ss of exon 7
cattaagggggatttttgataaactttttattatgaagtttt-----attttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
      ||    || ||  |  | ||||| || ||||  |||      || | ||   |  |  || |      ||   | |  | |  |   |    |  ||||| ||| |||||  ||||||| |||||||| ||||||||||| || ||  ||||||||||||| ||||||||  | || |||||| | |||||||||||||
-----gggtatgttattactggatttttttttctgaaacttttaagagttgttcaaactggtagggatgtactatatggtattgactagtaaaacatatgaatagGTTTACACATACATGGACGAGGCACACAGTATTGGAGCTGTTGGGAAAACAGGAAGAGGTGTGTGTGAGCTACTAGGAGTGGATCCGGCTGATGTTGACA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------------------cattaagggggatttttgataaactttttattatgaagttttattttccattttactt--tggttcattgtta--ctttgtgtatttt--ttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
                                                                                      |||    | ||  ||  | |    ||| | | || ||||||   | |||  | |   |   |  ||  |    ||||  |||| |  ||  ||| ||  | ||||||| |||||||| || || |||||||||||||| ||||| || ||| |||| ||||||||||||||  |  | || |||||  | || |||||||| |
gttcaagaatttcttacactgacttcttgtatatgttctttcttcagatcattaagcatgtaaatctttttttaatcaaaagcttgtaaatctgtttactgtcatatacattact-tcaacttttatcagctattaaaatcgataaatatttactgagttttgactattgtacttaaatttctggacagGCTTACACATATTTAGATGAGGCACACAGCATTGGGGCTGTTGGTAAGACAGGGAGAGGTGTTTGTGAATTACTTGGAGTGGACCCAGCGGATGTTGATA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 7
cattaagggggatttttgataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgt---attttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
     |      ||| |||   | ||| ||  |   || ||     |   ||  |   ||| |   |   |    | |    || |    ||    |  | |||| || |||||| | |||||||||||||| ||||||||||| || ||  |||| |||||||||||||||||  | || |||||| | |||||||||||||
---acataccagtttatgactcagtttatagaaattagattctcagtttcttaaaaactgggttgcttccaaacagggcctaatatacctcacatatgaacagGCCTACACATATCTAGACGAAGCACACAGTATTGGAGCTGTTGGGAAAACAGGGAGAGGTGTTTGTGAGCTGCTCGGAGTGGATCCAGCTGATGTTGACA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------------------cattaagggggatttttga-taaactttttattatgaagttttattt-tccattttactttggttcattgttactttgtgtattttttccattgct----ttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
                                               ||||||        |  | |||||| |   ||   |  |   | || || |   || |||| ||   || | | |    ||  || | || |  |    ||  |||| |||   || ||||||||||| ||||||||||||||  | |||||| ||||||||||||||||||| ||| | || || || ||| ||||||| ||||
gtgaggcaacataataaatcatcttttatgttcaacattgatgagagattaagaaactcaatcaactaaactatcatttgcaacatcaaagttgtctagactaatttgattgtctgatgcgtaacttaacttcttcaatattcttgtttcagGCATATGTTTACTTGGACGAAGCTCACAGCATTGGAGCAATTGGCAAGACAGGAAGAGGTGTTTGTGAACTCCTTGGAGTTGACACTTCTGATGTGGACA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G48790.1 (Arabidopsis thaliana), 3'ss of exon 3
cattaagggggatttttgataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
         ||     || |||||  | | | |  |  |     ||      | | |  ||| |  | | |  |    |||      ||||   ||  |||| |||   |||||||||||||| || |||||||||||  | |||||  ||||| ||||||||||||| ||| | || || || ||| |||| || ||||
-----gtaaggtaacatggtaaaccatctttca--agatcaacattgatgagtgattaaggtactctatcaactgaattat------cattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 7
cattaagggggatttttg-ataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
  ||    |   ||| |   | ||   ||   | ||    |||  |||||      |     |   || | |   |     |   ||| |     || ||||| ||| | |||||||| || || |||||||| || || || || ||  ||||||||||||||||||||||||| || |||||| |||||||||| || |
ttttcgttgctttttctatgtgaatagttctctttgtctctttcctttccgccccccccccctctcttttgagcattcac-tacattcaaccctgttgtagGCATATTCCTATTTGGATGAGGCCCACAGCATAGGTGCAGTTGGGAAAACAGGAAGAGGTGTTTGTGAGCTCTTAGGAGTGGATCCTGCTGATGTGGATA

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|17400406|gb|BM177188.1|BM177188
EST:     GAGAGCTTTGCAAACTTCCAGAGGTCATAGCTGTATGTAAAAAATACAAG                         GCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCA
genomic: GAGAGCTTTGCAAACTTCCAGAGGTCATAGCTGTATGTAAAAAATACAAGgttggtaatt ... tgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCA
EST: gi|17519162|gb|BM188204.1|BM188204
EST:     GAGAGCTTTGCAAACTTCCAGAGGTCATAGCTGTATGTAAAAAATACAAG                         GCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCA
genomic: GAGAGCTTTGCAAACTTCCAGAGGTCATAGCTGTATGTAAAAAATACAAGgttggtaatt ... tgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
                                   ttttttccattgcttt  CT-rich tract
                           tttgtgtatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattaagggggatttttgataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - aaggggg
- - - - - - - - -gataaac
- - - - - - - - - - - - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgtg