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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

Basic information

species Glycine max
transcript GLYMA04G39920.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 ||      ||      ||  |   | |   | | |     |  || |  ||   ||   | |||| ||   |  |  |||| |     |   ||| |||||||||||| |||||||||||||||| |||||||||||| |||||  |  | || ||||| || || |||||| ||   ||||| ||  |   ||||||||
gtaactatttttttgttttccttttgatcactat-tatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt---atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 |||  |    |||||         |    |         ||| |||   |    |   || | |    | |     | | ||||||||| ||   |  | ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| ||||| || ||||| ||||||   ||  ||||  |||  || ||||
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaag---ccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------tattgcacttga-aagctttataaaggtggttgtctgcttttttcattcctgggctatcatttt-ttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
                                                                      |||||      || ||||  |   |    |      |  | | |||   |   ||   || | |    |     | | ||||||||| ||   |  | ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| || ||||| ||||| || |||   ||  ||||  | |  |||||||
gtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaag---ccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 4
--tattg-cacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
  | |    |     ||||||| |     ||  ||| |   | |        || | |    |||| |  |  |     ||   ||| |   ||     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || || ||| ||   ||||||||  ||  ||| || |
cctgtaaataagcagaagctttttcctcttg-ctgtgtaactctaatgcatttgagtttctgttttgtggtcagtttctgtaatctttaaccgt--tcatcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCAACCCAACTGCTTTACCAGTCTTGCCCTTACCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
-tattgcacttgaaa-gctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt-atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
   |  ||||||    | |||      |  |       || ||        |  | |    ||||||  | ||  | |    ||||| ||   |     | |||||||||| |||||||||||||||| |||||| || || ||||| || || || || || || || |||||| ||   ||||||||  ||  ||| || |
tagtaacacttggtgtgttttcctcctgctgcatataactcttaatgcatttaagtttctgtttttttgtctgttcctgtaatccttgaccgttca---tcagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggc-tatcattttttat-----ttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
 |||   |     |  ||||       |  |||  |  || |||||    |     |||| | | |||      || |     ||   |||||| | | |     ||||||||||||| ||||||||||||| ||| ||||| ||||| |||||||||||||| || || ||||||||||||   || || ||  || |||| ||||
gtatcctatgcctagcctttg-gtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------tattgcacttgaaagctttataaaggtg--gttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
              ||||    ||      |  |||    |    ||  |   |  ||    |     |   || || ||    | |     ||   |||||| |||    |  ||||||| ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||||   || || ||  |  |||| ||||
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

upper sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
-tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
    |||| ||    | || |  ||     |  |||      |   ||  ||   ||  | | |||| |   |  |   |  |||||  |||  |||||||||||| ||||| ||||||||||||| |||||||||||| || || || ||||||||||| ||||| |||||||||   || ||||| ||| |||| ||||
aggctgcatttatgtgtttcaataactatttcctctagggcctgtctttgtgttgtaataatgtttagtcttgt-ttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

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|9440372|gb|BE440878.1|BE440878
EST:     GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATTgtatccttaa ... tggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
EST: gi|254319936|gb|GR829232.1|GR829232
EST:     GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATT                         ATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG
genomic: GCTCTTTCTTATCTTTTCTTGCAGTGATTACAACTTGTGTTGCTCAGATTgtatccttaa ... tggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT
                                 gtccttaac  putative branch site 
                                                ctttt  putative PPT
         tatcattttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

- -tgcactt
- - - - - - - - - - - - ggtggtt
- - - - - - - - - - - - - - - - tctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttaac