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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA

Basic information

species Glycine max
transcript GLYMA03G07890.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
--taccaagt-catgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
  |      | |||   |  | | |  |  | ||      ||| | | || | ||    || |    |  |  |  | | ||  ||  |     | ||| ||||||||| ||||||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || | ||||| ||||||||||| 
tttgttggtttcatcaaccttgcttcctccataacat--atgcatacctgctgattatctgtta-attttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtg----tgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
  |      ||   ||    ||  |     | |       |||||||||| |    |        | ||   ||      |  ||     | ||   | | ||||||||| ||||||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| | || |||||||||||||| 
--catgagtattgactgcctatttttgtcgacttcaca--tttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 11
taccaagtcatgttctatacatagtgaaaaattgtggtgc-tttcatgat---aatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
       |    || | |   |  |||    |      |  |||| ||||   ||  ||||  |    ||||  | ||  |  ||   |    ||  | | ||||||||| ||||||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| | || |||||||||||||| 
--tttgattggtttatttggctgctgagctttgtcttcgtatttcgtgatcgaaaaatcatcttaatctaactaccat--acttttcctgccatatgtgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
--taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagtt-cagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
     |   | |  |   |||  |   |  |  |  | |       |  ||  | | |   | |  |   |     ||   ||   | |   |    || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||| ||| |||| ||||| || ||||| 
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatg-tattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 11
-taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtg-tgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
 ||  |  |      | |    |  | | | |  |   ||||  | | | |||  |||| |  |  | |||        | |   |||  ||     | ||| ||||| || || ||  |||| |||||||  || || |||||||| ||||| || ||||| |||||||||||||| ||| |||| ||| | |||||||| 
ctattagatgtcaaaccaagacttttaatatacagc--tgctaccctcacaattacatgttaatcctcacagtctgagtaatgtggttcatttaaaatgcagCGTGATTCAATTTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------taccaagtcatgttctatac-atagtgaaaaa---ttgtggtgctttcatg------ataatgtcatggtgtgataa-----catcgatgaaagtt----cagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
                                       |    ||   |  |   || | |  |    |   ||   ||  ||| |||      ||| |  ||     || ||       ||| || |   ||      |  |  | |  |||||||||||| || |||||| ||||||||||||  |||||||||||||||||||| |||||||||||||||||||||||  |||| |||||    |||||||||
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactcttactgttattttatgtagaatatatttccagaccttggtagatgtttatctataatcattgttgttggctcctccaatttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAA

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ37798 (Selaginella moellendorffii), 3'ss of exon 11
taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
                                | ||   || ||| |||  | | | | | | | |||  | |      | ||       | || | ||||||||||||||||||||| | ||||||||| |  ||||| |  |||||  |||| || ||||||||||| |  ||  | ||||| ||||||||||| || 
-------------------------------gtatg-cactatcaagat--tctta-gctttcaaaactccaacttggataca-------aactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAGTCCCTTCGTGGAATCAAG

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ32053 (Selaginella moellendorffii), 3'ss of exon 11
taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
                                | ||   || ||| |||  | | | | | | | |||  | |      | ||       | || | ||||||||||||||||||||| | ||||||||| |  ||||| |  |||||  |||| || ||||||||||| |  ||  | || || ||||||||||| || 
-------------------------------gtatg-cactatcaagat--tctta-gctttcaaaactccaacttggataca-------aactctccagTGTGATCCAGTTCTGCTCTAAAGCATTTGCATTGTATGCGCGTGCAACCACAGCTCAAGAAATATTTGGTCTTACACTTGAATCCCTTCGTGGAATCAAG

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|18730359|gb|BM525833.1|BM525833
EST:     ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAGgttagtgtag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|58025422|gb|CX712163.1|CX712163
EST:     ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAGgttagtgtag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|58015128|gb|CX701870.1|CX701870
EST:     ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTTTGCTCCACAGCATTTGCNTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAGgttagtgtag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
EST: gi|192326624|gb|FK018496.1|FK018496
EST:     ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG                         TGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC
genomic: ATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAGgttagtgtag ... accttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
                tgataac  putative branch site (score: 2)
                                       ttttttaccttttc  putative PPT
                                     agtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - catgttc
- - - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg