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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

Basic information

species Glycine max
transcript GLYMA15G00380.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 3
-----------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                 ||| |  || | | ||| | ||    ||||  |   |||    |  |    | |||  | | ||     ||||||||||||| ||| | ||||| |||||||||||||| ||||| |||||||| ||  | || |||||||||| |   |||||  | || || |||||||| ||
gtatgtgctttcattttgtacctgtcctatcttttcattcaaatcttg-gcttcgtcggatggtaaagattcaaactt-ttctgaactgcagTTGGGGGGCTGTTGAATGCTACCTTTGGCAATGCGACTGAGATGATTATCTCGTTGTACGCATTGAAAAACGGGATGATCCGTGTCGTCCAGCAATCGCT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
------------gtatccctcttttatttccctttttctctt--aaggcccgtatcctcttttcaac--tcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
             | |   |  |||||  ||  ||      |  |   || ||   |  |     ||  |  ||  |  | |    |||||||||||| || || ||||| || || || ||||||||||||||||| ||| |||| ||||| |||||||     |||||  | || ||||| |||||  |
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G046480_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgcttt--ctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                                              || |  |  || |  ||   ||    ||||              | |  |||    || | |   | |   |||||||||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || ||| ||||||     |||||  | || || ||||| || ||
gtgtgttctttgctcccatgctgtgctacatttcctaaacaaatattagctttaattaacatctgcttagtacttactatttagtaaagatgtaaaaccttttcttttccttctaattgcagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGAGTCGTCCAGCAGTCACT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
-------------------------gtatccctctt------ttatttccctttttctcttaaggcccgtatcctctttt---------caactcactcgtgttgctttct----gcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                          ||||  || |       ||      | ||    |||    | |  |  | ||||          |||    |    || |  |||    | ||||||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || ||| ||||||     |||||  |||| || ||||| || ||
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaa----ctcactcgtgttgcttt------ctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
|||| |||||||   |       |  |  | |       ||     | | |       | |   || ||  ||      |||||||||| || || || ||||| || ||||| ||||||||||||||||| ||  |||| ||||| |||||||     |||||  | || || ||||| || ||
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                           ||||  || |||  |     | |  ||| |      || |    |||| |  |   |    |||  | |||||||||||||||| || ||||| |||||||||||||| || |||||||| || ||||| |||||||||||       |||||||| ||||||||||||||  |
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggat-ctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------gtatccctcttttatttc-------cctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttc-tgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                                                                  |  ||  |||| ||           | |||| ||  |   |  | | || |  |   || | ||   |||  | ||  ||||||||| ||||| || ||||| || ||||| |||||||||||||||||||| |  ||    ||  ||   |  ||||||||| | ||||| |||  ||| ||
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttc-tctcttgctaaaaagtaacctttgtgacctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------gtatccctcttttatttccctttttctcttaaggcc---cgtatcctctt--ttcaactcactcgtg-------------ttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                                               |     ||||  | |      |      || || |    || |     |  ||||| || ||   |             ||||| | ||||||||| ||||| || ||||| |||||||| |||||||||||| ||||||| |   |    ||  |    |  || |||||| | ||||| ||   ||| ||
gtgattgccgaagttcgaatgttgctgccttatgaagcatattggtttgcatttcttgcaatctgtgctgcagaataggggcaagtgtgtttggctgattcaattctctgacgaagaaactgatctttgctatttgcagTTGGAGGTCTCCTGAATGCGACCTTTGGAAATGCAACTGAAGTGATTATTTGTGTCATGGCTCTCCGGAAGAACATGATACGAGTTGTACAATTATCACT

upper sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
------------------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttct-gcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                        |      |  || |||   ||    ||| ||   | |     ||||   | |   | | || ||  |  || |||||||| ||||| || ||||| || |||||||||||||| |||||||||||||  ||   ||| ||    |  || |||||| | ||||| |||  ||| ||
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

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|213610489|gb|DB958794.1|DB958794
EST:     GCAGCTTGCCTTCTACACAGGACCCACAG                         TTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGANATGATTATAT
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatccctct ... ctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATAT
EST: gi|213614610|gb|DB972850.1|DB972850
EST:     GCAGCTTGCCTTCTACACAGGACCCACAG                         TTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAAC
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatccctct ... ctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAAC
EST: gi|209711678|gb|BW674041.1|BW674041
EST:     GCAGCTTGCCTTCTACACAGGACCCACAG                         TTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATAT
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatccctct ... ctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATAT
EST: gi|209715667|gb|BW674353.1|BW674353
EST:     GCAGCTTGCCTTCTACACAGGACCCACAG                         TTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATAT
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatccctct ... ctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
                              aactcac  putative branch site (score: 2)
                                          ttgctttct  putative PPT
                         ttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA