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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttcctttttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT

Basic information

species Glycine max
transcript GLYMA11G05760.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G157820_T02 (Zea mays), 3'ss of exon 11
tacacggatattttattgtgacttgcc--tacctgacagcacatgcatccaacatccgtta-attcctgtgatgatttcctttttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
   |     || |       | |  ||   | |   | |   ||   |  |   | |   |  ||| | |  |||   | | |  |  || ||    ||  || || || || |  ||||||||||| ||||| || ||||| ||||| ||||| || ||  | ||||| ||||||||||||||||| || || |||||||| 
--aattagcatgtggcaacaattcaccaccatcctgctgt-tataattttatggttcaccatgttctttttgtgaaaacttatcccttcccttgtgcattcagGTGTCCAAAAATTTGCAAGAATCGTTTTCGAGGATGTCACTGTGCAAAGAGCCAGTGTCGCAGCCGCCAATGTCCATGTTTTGCAGCTGACAGGGAATGC

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G23380.1 (Arabidopsis thaliana), 3'ss of exon 11
tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttcctttttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
                 || |  |    | ||   |  |    ||||    ||   |||  |       | ||| ||      |    |||  | |  || ||||| ||||||||||||||| | ||| | || ||||||||||| || ||||| ||  ||||||| || |||||||| |||||||||||| ||||||||
-----------------gtaatgta---atctatgattatccacatctg-tatttcttagctttgaatctcattaccaacaaactatattttctgtgtagTTGCCCAAAGAGCTGCAAGAATAGGTTTAGAGGTTGTCATTGTGCCAAAAGTCAGTGTCGAAGCCGCCAGTGTCCATGCTTTGCTGCAGATCGGGAATGT

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 9
tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttccttt--ttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
 |      || |||    |    ||  | | |      | | |    ||   |   ||||| | |||||  ||   ||    ||      | ||  ||| |||||||| ||||| ||||||||||||||| | || || |||||||| || ||||| ||| |||| |||||||||||||| ||||| ||||| |||||||||
caagtctctaatttgagatattgtggtt-cattgttctagaggtgatcatgttatattaatgc-tgtgagaatagtctgaaatttttttctctctcatctagATGCCCTAAGAGTTGCAAGAATCGATTTAGAGGTTGCCATTGTGCCAAAAGTCAGTGCCGAAGTCGTCAATGTCCATGCTTTGCGGCAGACAGGGAATGT

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S100_146V6.1 (Physcomitrella patens), 3'ss of exon 12
tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttcctttttcccccttttcatatca---------------agATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
     |  |  ||  |    |  | |     | ||   | |||  |||  ||||    |   | || |  | || |    ||  ||||| |||| | |               || ||| ||||||||||||||||||| || || ||||| |||||||| |||||| | ||| | || || ||||| || ||||| |||||||   | || |||
---gtgagtgattcttacaaaagtccaacttttactata-atgtctcctgcatcga--agcccttggggaggttgctagcttttcccttatcatgtgacaatggtcaccatgcagGTGCTCCAAGAGCTGCAAGAATCGGTTCCGGGGCTGCCATTGTGCAAAGAGTAATTGCTGTAGTCGGCAATGCCCGTGTTTCGCTGCAGGGCGCGAGTGT

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|6566978|gb|AW234605.1|AW234605
EST:     AAGCAGTGTCCTTGTCTTCAAAATGGAACCTGCTGTGAGAAGTACTGTGG                         ATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAG
genomic: AAGCAGTGTCCTTGTCTTCAAAATGGAACCTGCTGTGAGAAGTACTGTGGgtaagctttt ... tcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacatccgttaattcctgtgatgatttcctttttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT
         cgttaat  putative branch site (score: 4)
                        tgatttcctttttccc  putative PPT
                                          ttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacacggatattttattgtgacttgcctacctgacagcacatgcatccaacatccgttaattcctgtgatgatttcctttttcccccttttcatatcaagATGCCCCAAGAGCTGCAAGAATCGATTTCGTGGCTGTCATTGTGCTAAGAGTCAATGCAGAAGCCGTCAATGTCCATGTTTTGCTGCAGATAGGGAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - tgacttg
- - - - - - - - - - - - -cctacct
- - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - ccaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtga