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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG

Basic information

species Glycine max
transcript GLYMA11G31470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 2
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttag-agcaacatcttcaaatcttccctgccattt-ttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
 | | | ||||  | |  |||   | | | ||  | |  | | | | | |    ||  ||  ||     |  |  |       ||   |||  ||  ||||||| ||  | |||||||| |||||||| ||| | |||||||||||||| || ||||| ||||| || |||||||||||||| ||||| |||||| | ||||
gctttatgttt--tggatgttgagacttcgtttgtagattttctatggtttttgggcatactagttcttttcttgatgaagttcttttattcatttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 2
-tcctaaagtttcctaggagtttcaaatccat-tgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
 |  |     ||| |||   | |    || |  | |   | ||   ||   |   | |  | |  ||||||     | || |       | |  | || ||||| ||  ||||||| |||||||| || ||| | ||||| |||||||| || || || || || ||||||||||||||||| |||||||||||| | ||||
ttagtggttattcgtagatatatgttgtcgacataaaaatttgcagttccttttttcggct-gttcaacattagtcagtcatattcttaactcct-ttgtagGGCCCTAGAATGGTGCGTGATGTGTTCCGTTTGGCTAAGGAGAATGCTCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatctt----ccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
 |||   ||   |    | |||   ||   ||  || | |     | | |||||   | ||  | |  |||| |  | ||     | | | | || | || ||||| ||  ||||||| ||||| || || ||| | || || |||||||| || || || || || ||||||||||||||||| |||||||||||| | ||||
-cctgtcgtggacataaaattttgcatttttttcttcttttcagct-gttcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
          |  ||  | |   |  |  |||||  || |  ||  |  | |  | ||          | ||       |  |||   |||| |||  |||| || || |||||||||||||| || ||||| || || || ||||| || ||||| || || ||||||||||| ||||| || || |||||||| ||||
---------gtattaaaaatcatagctttattgaaggtttaggtcctattgagcgattc---------tatttggtgactaactggttttttaattgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 2
--tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
     | || | |  ||    ||  | ||      ||  |   ||   |   |     |||  |   |  | |  | || ||   |  |  || |  |  |||||||  ||||||| |||||||| || ||||| || || |||||||| ||||| ||||| || ||||||||||||||||| || || || ||||| ||||
tggttttaattgttttatcttttctagatt-gccaatattgc-tgcaatacccttaaattttaatttatctatatatatattttttttctcttgttatcaagGGTCCGAGAATGGTCCGTGATGTTTTCCGTCTTGCCAAGGAGAATGCTCCTGCAATTATCTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 2
---tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
   |  ||     ||  ||||     |  |      || || | |||| |      | | || || | |  | |    ||||  | ||  | | |||||  ||||||| || ||||| |||||||||||||  || || || || ||||| || ||||||||||||||||||||  |||||||||| || || ||  | || |
gtattttatgcactctcaggaaacgtagttttga-aatggtctatgttataggacgtcggtt-gaactatgtttgagtatctcgcatgt-aatgttattacagGGTCCCCGTATGGTGCGTGATGTATTTCAACTGGCAAAGGAAAATGCCCCAGCTATTATATTTATTGATGAAATTGATGCAATCGCAACAGCCCGTTTCG

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 2
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagag-caacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
|  |   |     ||    ||||   ||   | ||      | ||     |   || |||    || | ||     | ||    ||  |   |||||  ||||||| || ||||| ||||||||||| ||||| || || |||||||| || || |||||||||||||||||| |||||||||| || || ||| | ||||
ttatgttgcaagataatcctttcgtttctggtaatcaatcattttaaaccctcgggcttattttcagcttcacttgaactcatgtgt-agccttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCAGCCATTATATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTG

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|254324498|gb|GR833923.1|GR833923
EST:     CATCATGGTTGTAGGATTTGAGTTTTG-GCCAAAAGTATCTTGGTGAG                         GGTCCACGATTGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
genomic: CATCAGGGTTGTAGGATCTGAG-TTTGTG-CAAAAGTATCTTGGTGAGgtatgatttt ... tttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
EST: gi|5677488|gb|AI938618.1|AI938618
EST:     CCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAG                         GGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
genomic: CCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAGgtatgatttt ... tttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
EST: gi|254324497|gb|GR833922.1|GR833922
EST:     CCTTCATCAGG-TTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAG                         G-TCCACGAATGGTTCGTGATGTATTTCCTCTCGCTAA-GAGAATGCGC
genomic: CCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAGgtatgatttt ... tttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGC
EST: gi|298195266|gb|HO043794.1|HO043794
EST:     CCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAG                         GGTCCACGAATGGTTCGTGATG
genomic: CCTTCATCAGGGTTGTAGGATCTGAGTTTGTGCAAAAGTATCTTGGTGAGgtatgatttt ... tttattttagGGTCCACGAATGGTTCGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG
 ttttgat  putative branch site (score: 4)
                               tcttccctgccatttt  putative PPT
                                          atttttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatcttccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG

- - - - - - - - - - - caaatcc
- - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcttc