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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttgggcatatgtggctccaaatgcgttctgaatattctggtactcagaagaacaggctatatattaatattcaccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA

Basic information

species Glycine max
transcript GLYMA13G01190.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 8
atctttgggcatatgtggctccaaatgc-gttctgaatattctggt-actcagaagaacaggctatatattaatattcaccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
        || ||| |   |||| | ||   |     |||| |  |   |||      |  | |    | |||  |   |  || || || ||   || |||| || || || ||||| ||  |||||||||| || ||  |||||||||||||||| |||||||| || |||||||  ||||||||   ||| |||| |||
gagggactgcttatatatatccagacgctagtgatgctattgtaattgatcaactattcttgtttgtcactaaagtgatcacttatcatattta--ttccagGGGGCATCGTGAACAATTCCCTACGTCCTCAGATCCCCTCATGGTGTGATCCTGAATGGAAATCACTGATGGAAAACTGTTGGGCCAGTGAACCAGCAGA

upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G450602_T01 (Zea mays), 3'ss of exon 2
atctttgggcatatgtggctccaaatgcgttctgaatat-tctggtactcagaagaacaggctatatattaatattcacc--attgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
|| | ||   || | ||  ||   |   ||  | ||||| ||| |         |       ||| |   |  | | | |  ||||   | | || |||  ||| || ||||| ||| | ||  ||||||||||||||||  ||||||||||||||||||||||     | ||||||||||||||| |   ||||||||  ||
atttatgttgatttttgaatcttta---gtcataaatatatctcgcctaggcttgttgttattatgtcacagcagtgatctgattgcaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGGTTGATGGAAAGTTGTTGGTCCAGTGATCCAGCTGA

upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G374044_T01 (Zea mays), 3'ss of exon 2
atctttgggcatatgtggctccaaatgcgttctgaatat-tctggtactcagaagaacaggctatatattaatattcacc--attgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
|| | ||   || | ||  ||   |   ||  | ||||| ||| |         |       ||| |   |  | | | |  |||    | | || |||  ||| || ||||| ||| | ||  ||||||||||||||||  ||||||||||||||||||||||     | |||||||| |||||| |   ||||||||  ||
atttatgttgatttttgaatcttta---gtcataaatatatctcgcctaggcttgttgttattatgtcacagcagtgatctgattacaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGGTTGATGGAAAGCTGTTGGTCCAGTGATCCAGCTGA

upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 7
atctttgggcatatgtggctccaaatgcgttctgaatat-tctggtactcagaagaacaggctatatattaatattcacc--attgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
|| | ||   || | ||  ||   |   ||  | ||||| ||| |         |       ||| |   | || | | |  ||||   | | || |||  ||| || ||||| ||| | ||  ||||||||||||||||  ||||||||||||||||||||||     | |||||||| |||||| |   ||||||||  ||
atttatgttgatttttgaatcttta---gtcataaatatatctcgcctaggcttgttgttattatgtcacagtagtgatctgattgcaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGATTGATGGAAAGCTGTTGGTCCAGTGATCCAGCTGA

upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G039106_T02 (Zea mays), 3'ss of exon 6
-atctttgggcatatgtggctccaaatgcgttctgaatattctggtactcagaagaacag--gctatatattaatattcacca--ttgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
 || ||| |     | |   |  |  |  ||  | |||||  ||   |  ||    |  |    ||| |   |  | | |  |  |||   ||| || | |  ||| |  ||||| ||| | || ||||| |||||||| ||  ||||||||||||||||||||||     | |||||||| |||||| |   ||||||||  ||
gattttttgttgagttt--ttgaatcttagtcataaatatattg---cctaggcttattgttattatgtcgcagaaatgattaggttgcaatacattttctctagGGGCCATTGTAAACGATTCCTTACGCCCTCAAATCCCTTCATGGTGTGATCCTGAGTGGAAGGGATTGATGGAAAGCTGTTGGTCCAGTGATCCAGCGGA

upper sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
------atctttgggc----atatgtggctccaaatgcgttctgaatattctggtactcagaagaacag-gctatatattaatattca-ccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
       |||  ||||     ||   |  |||  | ||  ||  |||    |  |  |  ||     || |  |   ||| ||    | |  |||    | |      || ||||  |  |||    |||  | |  ||   ||  |  |  |   ||    |   | ||  ||| |  | || |   | |   | | | |           
cattttctctaggggccattgtaaacgattccttacgccctc-aaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGC-GGAGAGACCGTCCTTCACTGAT-ATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATG--AATGTGAAGTGAAGGTTCGGAAGCCATATTTGT-------

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|27426723|gb|CA938243.1|CA938243
EST:     AGGGAATGAACCCTATGCTGATATGCATTGTGCTTCAATAATAG                         GAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC
genomic: AGGGAATGAACCCTATGCTGATATGCATTGTGCTTCAATAATAGgtgagaacca ... ttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC
EST: gi|16349330|gb|BI974925.1|BI974925
EST:     CCTATGCTGATATGCATTGTGCTTCAATAATAA                         GAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC
genomic: CCTATGCTGATATGCATTGTGCTTCAATAATAGgtgagaacca ... ttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC
EST: gi|151404424|gb|EV274234.1|EV274234
EST:     ACTCACAGGGAATGAACCCTATGCTGATATGCATTGTGCTTCAATAATAG                         GAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC
genomic: ACTCACAGGGAATGAACCCTATGCTGATATGCATTGTGCTTCAATAATAGgtgagaacca ... ttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcagaagaacaggctatatattaatattcaccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA
                    tattaat  putative branch site (score: 2)
                                           ctttgttt  putative PPT
                tatatattaatattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttgggcatatgtggctccaaatgcgttctgaatattctggtactcagaagaacaggctatatattaatattcaccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA