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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttataagaagaaatacaatatttatttatctggacaggatacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA

Basic information

species Glycine max
transcript GLYMA07G00950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 4
agttataagaagaaatacaatatttatttatctggacaggatacaagaatttccccctcttccatgcttga--cattg---tgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
               |  ||| ||  || ||||       | |      |||  | ||||   |   |  |  ||||       | | |||| ||  | |  ||||| || |||||||| ||||| || || |||||  |||||||||| || ||||||||||||||||| || |||||||||||||| ||||| ||||||||||
--------------gtttaatcttgtttaatctcccattcacattttc-tttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcagATATACGACATCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
agttataagaagaaatacaatatttattta--tctggacaggatacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
               |   || ||  |  |  | || |          |   ||  | ||  |     ||||   |||||    |||  | ||   ||||||||||||||||| || ||||| || ||| | || ||||||||||||||||||||||| |||||||| || |||||  | ||||| |||||||| |||||||
------------gtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
agttataagaagaaatacaatatttatttatctggacaggatacaagaatttccccctcttccatgcttgacat---tgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
                    |||  |  ||| |   |    |     |||| |   ||| |    | || || |   | | |    |||    | | || |||||||||||||| || ||||| || ||| | || || || ||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||||||||
-------------------gtatgcaaatattt---ctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------agttataagaag---aaatacaatatttatttat---ctggacaggatacaagaatttcc-----ccctcttccatgcttgacattgtgaaaattttggttggtgttg-cagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
                                                                              | || | |||||   |    || |  |||||  |    |   ||  ||     | |||       |  | ||   |   ||| | |     ||||||  ||| || || |||||||||||||| || |||||||||||||| ||| | |||||||||||||||||||| |||||||| || || ||||||||||| ||  ||||||||||||
gtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcagATCTATGACATTTTCCAGCTGCTGCCATCTAAAGTCCAGGTTGGAGTGTTCTCTGCCACAATGCCCCCTGAGGCCCTTGAGATCACTCGAAAGTTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------agttataagaagaaatacaatatttatttatctggacaggatacaagaatttccccctctt---ccatgcttgacattg--------tgaaaattttggttggtgt------tgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
                                           | |   ||||  |||   | | ||| | |  ||      | |     | | ||| |||  |   | |||   || ||||        | |  |  ||| || | |       ||||||| ||||||||||| ||||| || |||   ||  |||| || || ||||| ||||| ||||||||||| ||||| |||||||| || || ||||||||||
gtttgttcggagagtcctggaatggtagaagaaatttgtttttactcccaaga--aaactaattgtttgtgtgactatttcagttctctaattatcctccttataagctatgagagatattgctcaacgctaacgaaattgattcgggcatcttctgcagATTTATGACATCTTCCAGCTTCTTCCACAGAAGCTTCAAGTGGGTGTGTTTTCTGCCACAATGCCACCCGAAGCGCTTGAGATCACCAGGAAGTTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S136_29V6.4 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------agttataagaagaaatacaatatttatttat-ctggacaggatacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
                                                       || | ||| ||    || |||||   | || |||||  |   | | ||    |  |||      ||||| ||  |  |  || |||  ||  ||||||| |||||||| || ||||| || ||    ||  |||| ||||| ||||||||||| || |||||||| ||||| ||||| || || ||||| |||||||
gtgtgtaaaggatttttcaagttcagtagaacttgcatgatcttattgttcctggatgataaggaa-gtgatctttatacttgctcgacagc-tgtgaaagttggtgctgctta-----ttgac-ttaggtcagattgggtgagttgtgcagATTTATGACATTTTCCAGCTTCTTCCCCAGAAGCTTCAAGTTGGTGTGTTCTCTGCCACCATGCCACCCGAAGCTCTTGAAATCACCAGAAAATTCATGA

upper sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 3
agttataagaagaaatacaatatttatttatctggacagga-tacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgt-tgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
 ||  | ||  |    |  || |     | | | || |||  |    |    |    |  |   | |   | | |  |   | |  ||     |   ||||||| || ||||||||||||||||||||    ||  |||| || || || ||||||||||| ||||| || |||||||| ||||| ||||| ||||||||||
-gtgttgagtggtctgagtatgtcgcactgttttgataggggtgttggtgactgttacggtgaaaaggccg-cttacttgcagtgatgtccaatacgtgcagATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGA

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|17400917|gb|BM177699.1|BM177699
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|298195760|gb|HO044151.1|HO044151
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAC                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCA
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCA
EST: gi|21602355|gb|BQ612686.1|BQ612686
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|7590936|gb|AW706679.1|AW706679
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|13477731|gb|BG507492.1|BG507492
EST:     TGTTTTGGATGAGGCTGATGAAATGCTTTCACGCTG-TTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TGTTTTGGATGAGGCTGATGAAATGCTTTCACG-TGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|9566014|gb|BE475585.1|BE475585
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|9565591|gb|BE475100.1|BE475100
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|13789447|gb|BG652038.1|BG652038
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|26269229|gb|CA820292.1|CA820292
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAG                         ATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
EST: gi|14259432|gb|BG882340.1|BG882340
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt ... ggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA
                    gcttgac  putative branch site (score: 4)
                           attgtgaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttataagaagaaatacaatatttatttatctggacaggatacaagaatttccccctcttccatgcttgacattgtgaaaattttggttggtgttgcagATCTATGACATCTTTCAGCTGCTGCCATCCAAAATTCAGGTTGGAGTGTTCTCTGCTACAATGCCACCAGAAGCCCTTGAGATTACAAGAAAGTTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - -gaaatac