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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA

Basic information

species Glycine max
transcript GLYMA19G43400.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttt-tatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
       | |  | | |  || || || |     ||| |   |||||    | | |||  |  | |||      ||| |  |     ||| |||  | |  |||| |||||||| |||||  |||||||||||||||| || ||| | |||||||| || | |||||| ||||| |||||||||||  ||||  | ||||| |
-------gtttgtccatcaaaataattttaggctttagt---gttatgttttagtaaaaccagaagtt------gatttcctactgttttaactactgtccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttga--aaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                     |  |||  || |  ||   ||    | |  ||    | | |  ||      ||    || ||    |   ||     ||  |||| |||||||| |||||  |||||||||||||||| || ||| | |||||||| || | |||||| ||||| || ||||||||  | ||  | ||||| |
--------------------gtgtgttcatcgaaatacaatgacgttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
               || | |||| || ||  |  | |||| | ||   | ||   | | |||   |||   | ||| | ||| ||  |        ||||||| |||||||| |||||  ||||||||||||| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||
-------------gtttgtgattatttttt--atatgttcttgctaaagatttatgagt-cttttctta--tgtgatgt-tttgatgctga------tatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EDP09235 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatattt----gacttttt-----atagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
            | || |        |||     |    | || |  |  ||  |          | |  ||  | |   | | | |  |     || | ||       |||| |||||||| || || ||||||||||| || || || ||| | |||||||| || |||||||| || || ||||||||||| || | | | ||||| |
-----------gtcctctcggccgtgtgtctgcgtgtcgccggctgcttgctgcaccgcgacgccgctgtcactgctgattcttacacctcccaaacgtcttcgcccgcagCCCCAAGATGCGTACGGCCTGGAGAAGCTGGCCACCGAGGAGCTGTGCAAGCACTACAACAAGGACTTCGGCATTGAGTGCCGCATCGCGCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaa--tacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                   |      |  |   ||   |||   |  ||   || || |||| || |  || | ||  |  |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| |
--------------------------------gtatgaaaaagaaaaaaacaaaaaagcttcttttcttttgcgggga-atctgaaaaaatttgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTATGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37016 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                      | ||   |   |    |   |   |   | | | || |  | |  ||   |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
-------------------------------------gtatgtgaaagaaagaaatcctttctttctgatctggaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACGGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34003 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggtt---agcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                          ||   | |    | ||  |||   ||   | | |  |  | |  ||   |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | |||||| |||||||| ||||||||||||||| | ||||| |
------------------------------------------gtatgtgaaagaagaaccctttctttctgatctgaaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGACTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33664 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                      | ||   |   |    |   |   |   | | | || |  | |  ||   |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
-------------------------------------gtatgtgaaagaaagaaatcctttctttctgatctggaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37510 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggtt---agcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                          ||   | |    | ||  |||   ||   | | || |  | |  ||   |||  ||  ||  |||| |||||||| |||||||||||||||||    || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
------------------------------------------gtatgtgaacgaagaaccctttctttctgatctggaagttgtaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaa-tatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                           ||   |   |        |   |    ||  | |||   ||    |||  || |  ||  |  |  |  |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| |
---------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                   |||       |   |    |   |  ||   || || ||||       || |  |  |  |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| |
----------------------------------gtatgaaaacgaaaaaaaaaagcttcttttcttttgcggggaatctgaaaaaaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatat-atttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                   ||| |||  |    |    |||| |  | | ||  ||    | |  |||   || |  || ||| ||||| |||||||| ||||| || ||||||||    |  |||||| | |||||||| || | ||||||||||||||| |||||||||||||| ||||| || |
----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA

upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                |   |        |   |    ||| | |||   ||    |||  || |  || | ||  |  |||  |||| |||||||| ||||| |||||||||||    || |||||| | |||||||| || | |||||||||||| || |||||||| |||||  ||||||| |
------------------------------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|7232221|gb|AW567578.1|AW567578
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|213615128|gb|DB962840.1|DB962840
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|298163054|gb|HO011787.1|HO011787
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|151396815|gb|EV266688.1|EV266688
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATACAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
EST: gi|192324156|gb|FK017887.1|FK017887
EST:     AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG                         CCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG
genomic: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
                                       atttgac  putative branch site (score: 4)
                                             ctttttat  CT-rich tract
                            atatatttaatatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA

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