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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 12
aaattgaaccttcatttctctttccctagttagaatttactcatttggat-gtattattatttaagtaaatgacttgttcaaaatgaattcttttct---ccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
                |   |    ||||     || |||  || |  || || || |  |  ||    |    |||    || ||     || |      ||||||||| |||||||||||||||||||| |||| ||| ||  |||||||  | ||||| || || ||||||||||| |||||||| |||||
---------------gtaagtacttctag-----atgtaccgatgtaaattgtgttgtgctcaaaagggagtggttgacataactgcccctttctgcatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTTGTGTCATGGTATGACAACGAGTGGGGCTACAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 12
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
                | | ||   | ||  |       || |||| |   | | | |    | |||  |||  |    |  ||    | | |    ||||||||| |||||||||||||||||||| |||| ||| ||  |||||||  | ||||| || || ||||||||||| |||||||| |||||
-----------gtgactattttgatccagcgacgcaac-cttattttggcctgtgagttggaatgtagctgaaatcactatcattgcctttgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTCGTGTCTTGGTATGACAACGAGTGGGGCTACAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
              |  ||  |||  |     ||  | ||  | ||   ||   | |    |  | |  |  ||  |    | ||  |||| |    ||||||||| |||||||||||||||||||| || | ||| ||  |||| ||  | ||||| || || ||||||||||| |||||||| |||||
-------------gtgactacttcaatccagtgacgtaacctaattt--tgccctgtggggtgggaaggtagctgatc---attgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 12
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgt----attattatttaagtaaatgacttgttcaaaatgaattct----tttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
         ||| | ||| |     | |    || ||   | || |  || |    |  || ||||  ||  || ||   ||  | |||   |||    | | | |||||||||||| |||||||| ||||| || || |  || |||||||||||  | ||||| ||| | ||||||||||| || ||||| |||||
-------ttcttgaattcccaggatcgaacctgatttattttatctacattttcaaagcatcatttg-gtggatcaccatttttatatgttctctgctttatttacagGTCAAGTATATTTGATGCAAAGGCCGGGATAGGGCTGAGTGCTTCCTTCATGAAGCTCGTTGCATGGTATGACAACGAATGGGGATACAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S309_73V6.2 (Physcomitrella patens), 3'ss of exon 10
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
    |     ||  |   | ||      |  ||| | |  |  || | ||   | ||  ||    |     |||| |    | |||| ||||   | |||||| || ||||| ||||||||||| || |||||  | ||||     ||||| |||||||| |||||||||||||| |||||||| |||||
---gtaggtttttgtcgattttcgatgggacagattgtgtttgtt-gaattggtcatgtttgggat-----acttatg-gtattgaactcttga-tacagGTCGAGCATCTTCGATGCCAAGGCAGGAATTGCCTTGAGTGACAAGTTTGTCAAGCTGGTGTCGTGGTATGACAACGAGTGGGGCTACAG

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|151403747|gb|EV273557.1|EV273557
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|208123988|gb|GD925506.1|GD925506
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGGTGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|17022180|gb|BM093214.1|BM093214
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|6914527|gb|AW396057.1|AW396057
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|15589578|gb|BI674194.1|BI674194
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|51334832|gb|CO978698.1|CO978698
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
EST: gi|22927146|gb|BU544285.1|BU544285
EST:     GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG                         GTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT
genomic: GGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatg ... ttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG
                                          ttcttttctcc  CT-rich tract
      tattattatttaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - -accttca
- - - - - - - - - -ctttccc
- - - - - - - - - - - - - - - - - - - - - - -tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc