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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA

Basic information

species Glycine max
transcript GLYMA03G40720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttat--agCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
       | |  | | |  || || ||  | | | | |  || ||||    |   |||  |  | | |      ||| |  |    |||| |||  | |  |||| |||||||| |||||  |||||||||||||||| || ||| | |||||||| || | |||||| ||||| |||||||||||  ||||  | ||||| |
-------gtttgtccatcaaaataatt--ttaggctttagtg-ttatgttttagtaaaaccagaagtt------gatttcctactgttttaactactgtccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
       |    ||| | ||| |||      | |   |||  |||  | |   | | ||||  || | |      ||    |   | ||  || |||  |||| |||||||| |||||  |||||||||||||||| || ||| | |||||||| || | |||||| ||||| || ||||||||| | ||  | ||||| |
-------gtgtgttcatcgaaataca-----atgacgttcctgtttgttagacatatatac--agtcaaatctaaatcccctcggtgtt--acgttt-cagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
               ||   |||| || ||  |  | |||| | ||   | |||  | |  ||   ||     |   || |||   |  |||    ||||||| |||||||| |||||  ||||||||||||| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||
-------------gtttgtgattattttttata--tgttcttgctaaagatttatgagtcttt--tcttatgtg---atgttttgatgctga----tatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EDP09235 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaattttt----gactttt------atagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
            | || |        |||    ||    | || |  |  ||  |          |||  ||  | |   | | |    |     || | |        |||| |||||||| || || ||||||||||| || || || ||| | |||||||| || |||||||| || || |||||||||||||| | | | ||||| |
-----------gtcctctcggccgtgtgtctgcgtgtcgccggctgcttgctgcaccgcgacgccgctgtcactgctgattcttacacctcccaaacgtcttcgcccgcagCCCCAAGATGCGTACGGCCTGGAGAAGCTGGCCACCGAGGAGCTGTGCAAGCACTACAACAAGGACTTCGGCATTGAGTGCCGCATCGCGCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                           ||   |   |        |  ||   ||   |  ||    | || ||||       ||  ||||   |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| |
---------------------------gtatgaaaaa---gaaaaaaacaaaaaagcttcttttcttttgcggggaatctgaaaaaatttgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTATGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37016 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                               | || |        | ||  ||     |   |   || | ||   || |  |  | |||     ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| |||||||| |||||| | ||||| |
-----------------------------gtatgtgaaagaaagaaatcctttc----tttctgatctggaagttctaaaactcttgttt--tccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACGGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34003 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggct---agcagggatatatttaatttttgactt--ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                                          ||   | |   || ||  |||    |   | | |  |  | |  || | |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | |||||| |||||||| |||||||| |||||| | ||||| |
------------------------------------------gtatgtgaaagaagaaccctttctttctgatctgaaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGACTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33664 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                               | || |        | ||  ||     |   |   || | ||   || |  |  | |||     ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| |||||||| |||||| | ||||| |
-----------------------------gtatgtgaaagaaagaaatcctttc----tttctgatctggaagttctaaaactcttgttt--tccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37510 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggct---agcagggatatatttaatttttgactt--ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                                          ||   | |   || ||  |||    |   | | || |  | |  || | |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| |||||||| |||||| | ||||| |
------------------------------------------gtatgtgaacgaagaaccctttctttctgatctggaagttgtaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaattt--ttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                           ||   |   |        |   |   |||  | |||    |    |||  || |  ||     |||   |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| |
---------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcaggga-tatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                                   |||       |   |   ||   |  ||    | || |||| | |    ||   |||   |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| |
----------------------------------gtatgaaaacgaaaaaaaaaagcttcttttcttttgcggggaatctgaaaaaaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaat--ttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                                   ||| |||  |    |   ||||| |  | |  |  ||    | |  ||  |  | |||   ||| ||||| |||||||| ||||| || ||||||||    |  |||||| | |||||||| || | ||||||||||||||| |||||||| ||||| ||||| || |
----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA

upper sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                               | |  |        |   |   |||  |  |     | |  ||||       ||  ||||   |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || ||||||||||||||  ||||||| |
-----------------------------gtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

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|207699910|gb|GD682569.1|GD682569
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtatgttgct ... acttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|298178228|gb|HO023963.1|HO023963
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtatgttgct ... acttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|208115132|gb|GD911763.1|GD911763
EST:     GGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: GGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtatgttgct ... acttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|298189854|gb|HO038257.1|HO038257
EST:     GCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: GCCTGGCCTGCTGAGgtatgttgct ... acttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA
                                        ttttgac  putative branch site (score: 3)
                                              cttttat  CT-rich tract
                             atatatttaatttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT