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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

Basic information

species Glycine max
transcript GLYMA20G34940.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 8
cattaaaaagtgaccattctg-tattcatgagatgctaatccagattc-----ctggaacgtctgaaaatcataacttacgacccact----atatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
       |||  | |||| || | ||  | | | |  || |    |||     |     | |||     |  |  | | |  ||   |    ||   || | || | ||| |  |||||  |||  |  ||||  | || ||||| |||||| | |||  ||||||||||||||||||||| || ||||| |||||||| || || || |
-----gtaagaaagcattttgatgtttcttataagtgaaccggagttctcattccatgtcttctagtccttgtgccatccagcctttttgtcatcctttctattttgcagATCCCTTGGCGAGAAGTGGCAATTATGCCTATTCAGTGGCATGCCTTAGCTCTTGGCTTGTTTGCTTCAATAATAGCACCATTTGGAGGGTTTTTCGCTA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
------cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
         |     ||    ||| ||| ||  |   ||| |  ||||       |     | ||      | |  | |  |   | || ||||  | ||  ||||||  ||||||| ||  |     |  | ||  | || |||||| |||||   || || |||||||| ||||| || |||||||||||||| ||||||||||
ctgtttttgtttttcgtttgaattttgttttt-tatcatgttt-tccaagcaatggatgtttttgg---ctaaagttaataagttattacatgtattgttg-acagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G062416_T02 (Zea mays), 3'ss of exon 3
cattaaaaagtgac-cattctgtattcatgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
  | || |||  |  |   |   | |||  |  |   |||    | |  |   |   |      |  |      | |   | | ||| ||||  | |||||||| | |||  ||| ||  ||||  | ||  ||||||||||| | |||  ||||||||||||||||||||| || ||||| ||||| ||||| |||||||
-gtaaataagcaattcgagcctaactca--aattctcaattggaaatggttacattccatctgttgctgttgctccaattagtttat-ttgtactgtacagTTTCCATGGCGAGAAATTGCAATTATGCCCGTTCAATGGCATGCATTAGCTCTTGGCTTGTTTGCTTCAATAATAGCACCATTTGGTGGCTTTTTTGCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaat-cataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
   |    ||  | ||    ||| |  |    ||       ||  |    |   |  | | | | ||| |  |    |    |    |||   || | |||||| ||||||| || ||  | ||||| ||  |||| |||||| ||||||| || || ||||| |||||||| || |||||||||||||| || || || |
-tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 9
cattaaaaagtgaccattctgtatt---catgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
   |  ||||  |    ||||  |    |||| |||   |||    | ||    ||        | | |     | |  | | ||     || |||| | |||||| ||||||| ||| | || ||  ||||| |||| |||||| |||||||| | || |||||||| ||||| || |||||||||||||| || |||||||
---tgtaaagctattcctctgattaaagcatgggatttaaattttcaatctcaaaaaaaagatcagtaactctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA

upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 8
cattaaaaagtgaccattctgtatt---catgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
   |  ||||  |    ||||  |    ||||||||   |||    | ||    ||        | | |     | |  | | ||     || |||| | |||||| ||||||| ||| | || ||  ||||| |||| |||||| |||||||| | || |||||||| ||||| || |||||||||||||| || |||||||
---tgtaaagctattcctctgattaaagcatgagatttaaattttcaatctcaaaaaaaagatcagtaactctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA

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|6483173|gb|AW202361.1|AW202361
EST:     CCCTTACAAGGATGGATTTCCCACTGG                         TTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGT
genomic: CCCTTACAAGGATGGATTTCCCACTGGgtaagcactt ... tcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGT
EST: gi|151412323|gb|EV282135.1|EV282135
EST:     CACTGTTTAAGCCGGAATCTTATCCCTTACAAGGATGGATTTCCCACTGG                         TTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGT
genomic: CACTGTTTAAGCCGGAATCTTATCCCTTACAAGGATGGATTTCCCACTGGgtaagcactt ... tcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGT
EST: gi|208187913|gb|GD980973.1|GD980973
EST:     CACTGTTTAAGCCGGAATCTTATCCCTTACAAGGATGGATTTCCCACTGG                         TTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATG
genomic: CACTGTTTAAGCCGGAATCTTATCCCTTACAAGGATGGATTTCCCACTGGgtaagcactt ... tcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA
                      aacttac  putative branch site (score: 2)
                                          ttgtctt  putative PPT
              aaaatcataactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
-attaaaaa
- - - - - - -ccattct
- - - - - - - - - - - - tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacccac