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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag

Basic information

species Glycine max
transcript GLYMA05G30140.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 1
AGATCGATCGAA--CATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttc---ttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag--------
   ||  || ||  ||||||||| ||||||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||||||||| || |||||||||||  |  | |  |  |   |  || ||||||   || || ||  ||   |     |  | |       | ||   |      |   ||  |         
--CTCCCTCAAAATCATGGATGAAGAGTACGATGTTATAGTGTTGGGCACCGGTCTCAAGGAATGCATCCTCAGTGGTCTTCTCTCCGTAGACGGCCTCAAGgtcttcatcctttctaattcactcatttttcaacttctccttggaaataagaggttttttggccctctactggagtcatgcttgtaatcgactatttttg

upper sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgt---tcgattcag
                 | |||||||| || ||||||||| ||||||||||||| |||||||||||  |||| || || || || || ||       ||||| |     | |  |||      ||      |  |     |   |   |   || ||||  |||    |||     | |      | | |||
----------------AACGAGGAGTATGACGTGATCGTGCTGGGCACGGGTCTGAAGGAGTGCATCATCAGTGGCCTGCTGTCGGTGGACAAGAAGAAGgtgcgggacctagacatg-----cgcgcgaatgctgcaaccgggcctgcttttcttcgcgcgctggccgctcaccatcgcaacctgttgcag

upper sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 1
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttca------atcgatcca-atcctcgcatgctaattgc-tatttcttgttcgattcag---
 |     |     |||||||| || || || ||||| ||| | ||||| || |||||||| ||||||||||| || || |||||||| ||| ||||||||||    | ||| | | ||  | | | ||  | | | | |            |||  | | | |||| | |   |||  | |||    | | | |  |   
CGGCACCTTCGCTATGGATGAAGATTATGACGTGATTGTGCTCGGCACTGGCCTCAAGGAATGCATTCTCAGTGGACTGCTCTCCGTTGATCGCCTCAAGgtggcgtctccctccctcgatctgggttgacatgtgtgtgtgtagcttggagattgatagcttcgcgttcaggttgaatgtttgagatgcaagtgtgctg

upper sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
lower sequence: PP1S167_1V6.1 (Physcomitrella patens), 5'ss of exon 1
-AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag--------------
  || |   | | ||||||||| |||||||||||||| ||| ||||||| || || ||||||||||| ||||| || || |||||||| ||| | ||||||||     |   ||     |   | |||  ||| |     ||   || |     | | ||   |   |  ||   | | |   |  |  |              
TGGAGCCGGC-ACCATGGATGAAGAGTACGATGTGATTGTGCTGGGCACCGGGCTGAAGGAGTGCATCCTCAGTGGGCTACTCTCCGTGGATCGTCTCAAGgtg--ggtgggatcgcagatcgtggttgatctgtgtgactcgggcggtgtgg-cgtagctgccggctctctgggtgtagcgtggatttgtggtcggcgaggga

upper sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
lower sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag
   | | |    |||||||||||||||||| || || ||| |||| |||||||||||||||||||| |||||||| || || || || ||| | ||||||||    |||   |  |||    | |     | | ||| |   |                                              
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgg-gtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------

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|192322711|gb|FK014402.1|FK014402
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|193659253|gb|FK605052.1|FK605052
EST:     CTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGTGGAGAATCCACTTCGCTC
genomic: CTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213598704|gb|DB964270.1|DB964270
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|17021940|gb|BM092974.1|BM092974
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCTCTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213593669|gb|DB971691.1|DB971691
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|193325776|gb|FK290215.1|FK290215
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213590255|gb|DB963832.1|DB963832
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|193590886|gb|FK548231.1|FK548231
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|151400876|gb|EV270690.1|EV270690
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|209722563|gb|BW682662.1|BW682662
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|17964174|gb|BM270913.1|BM270913
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACTTTTATGAGAATCCACTTCGC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTAC--GGAGGAGAATCCACTTCGC
EST: gi|213603679|gb|DB966807.1|DB966807
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|254342789|gb|GR858951.1|GR858951
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|209710882|gb|BW653643.1|BW653643
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|151400851|gb|EV270665.1|EV270665
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|208182856|gb|GD981050.1|GD981050
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213595671|gb|DB972141.1|DB972141
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttc ... ttcgattcagGTTCTGCATATGGATAGGAACGACTATTACGGAGGAGAATCCACTTCGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG