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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcc-tatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                       | ||  ||||      ||||  ||    || | ||  |  | |   | || |||     || |   ||     | |||     | ||   ||  ||  |   | ||||| |  |    || ||| ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||||||   |||||| ||| | |||||||| ||||| || || ||
--------------------------------------gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacatacaagtctgcagttcattcattgttttctttcattac---tgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccattt---ttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                                              |  |||    | |  |||  | || ||   |  ||| | | ||  |||    |      |||||     | |  ||     ||  ||       |    |||| ||| | |||| ||| |||||||| ||||| |||||||| ||||| |||||| | || |||||||| || ||  |||| || || ||||||||||| ||
-----------------------------------------------------------aaatgaagg---atacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagtt--gccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                                       | | |  ||  |||     |  ||   |||   |   |  |   |||        |||  |||         |  ||    | |   | | | |   |   |  ||| || ||||| ||||| |||||||| |||||||||||||| ||||| |||||  |||||||   |||||||||| | |||||||| ||||| || || ||
------------------------------------------------------gtatctacttggggc-----catctgaatctgtcgggaatctgataggggcaagtctgcagttt---------agctgaccattttgttgtctaatgcatgctttagGGAAGAAGTTCCATGACATTGTTGGAAGTGCTTACTATGTCGCACCAGAAGTACTAAAACGACGGTCTGGTCCTGAGTCAGATGTTTGGAGCATAGGAGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatct-----ttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                                                                             ||||  ||  | |   ||   | ||||  |||| || |   ||  |  ||||     ||    || |||| ||| ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||| ||| || ||| |||||||||||||||||||||||||
---------------------------------------------------------------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcagg-catgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                                                                  |      || | || ||| | | ||  | ||  |     ||   ||||     |     |   ||||  ||||   ||||||   || ||||| ||||| || || || || ||||| ||||||||||||||||| ||||||| ||| || ||| ||||||| || ||||||||||||||
---------------------------------------------------------------------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtagataa---tggaggtgattttgtgaaaatg-gcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgag----ttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                      ||     |  | |  | || ||  |   |  | |||    | ||   ||  ||     |||||   ||| |     |||  |   |||||  |  | |||  ||| || |           ||   | |||| ||| |  |||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| || | ||| || || || ||| |||||||||| ||||||||||||||
----------------------gtaagtgaaatttcgccttctcaatatatggactttgaaatccatattt--tcatgggtttctgttgttcaaacaattacaacatatgcttctagcttttgaattggaaaaa---------ctgaatatgaataaaca--cagGGAAGAAGTTTCAAGATATTGTTGGTAGTGCCTACTATGTTGCTCCTGAAGTATTGAGACGGAAATCGGGACCTGAATCAGATGTCTGGAGTATTGGTGT

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S83_172V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatg-cagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
                                                              || |     ||  |  |   |  |||      ||   |  | |  |  |  || ||| |   ||   |     |    | |         |  |||  ||| ||   ||||| |||| | || || || ||||| || || || || || || |||||  | || ||||||||| ||||||||||||||||||| || ||
-------------------------------------------------------------attgaatgacgtatttgt-cgtgatcaagaagatttctaaccttcatagtttcactttcagaggattctgaccctctcttttaaccatgccatgatgatagGTAAGCGGTTTCGTGATGTCGTGGGAAGCGCTTATTACGTGGCTCCAGAGGTCTTAAACAGGAAATCTGGTCCTGAATCAGATGTGTGGAGTATCGGAGT

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|193524793|gb|FK482328.1|FK482328
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193473081|gb|FK436670.1|FK436670
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193496517|gb|FK460703.1|FK460703
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         G-AAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193668943|gb|FK612271.1|FK612271
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|208080484|gb|GD878996.1|GD878996
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193451498|gb|FK417946.1|FK417946
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTACATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAA
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTT-CATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAA
EST: gi|193661924|gb|FK606938.1|FK606938
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193569503|gb|FK523118.1|FK523118
EST:     TTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCAATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTTAAAGGCCACTGATTTTGGTTTGTCAGATTTC-ATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193477388|gb|FK443525.1|FK443525
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|208072384|gb|GD872738.1|GD872738
EST:     CCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: CCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|193674208|gb|FK617300.1|FK617300
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|208335276|gb|GE135895.1|GE135895
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
EST: gi|208035511|gb|GD837255.1|GD837255
EST:     TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCGGATTTCATAAAACCTG                         GAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG
genomic: TTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTGgtgagggaaa ... aaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
        atttttatttgagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG