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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccctccgctaaccctaaccctaaccctcttttcttcttttcaattccttacttctcttctatttcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gtaccctccgctaaccctaa--ccctaaccctcttttcttct-----tttcaattccttacttctcttctatttcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG
                       || || |    |||   | | |   ||||    |       |||    |  | || |   |    |||  |||||||||||||||||  | ||||| || || ||||| ||||| || || || ||||| ||||||||||||||||| ||||| |||   || ||| | || |||
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
















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|17401363|gb|BM178145.1|BM178145
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|213594416|gb|DB970010.1|DB970010
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|15285225|gb|BI469116.1|BI469116
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCTTTTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|37996482|gb|CF808071.1|CF808071
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|37997640|gb|CF809229.1|CF809229
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|19269340|gb|BM885596.1|BM885596
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|5509172|gb|AI855730.1|AI855730
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|6912974|gb|AW394562.1|AW394562
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|151403300|gb|EV273110.1|EV273110
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|213617885|gb|DB957366.1|DB957366
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|298197166|gb|HO041909.1|HO041909
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|213599336|gb|DB972278.1|DB972278
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|298180890|gb|HO022329.1|HO022329
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|7588108|gb|AW703911.1|AW703911
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|37997219|gb|CF808808.1|CF808808
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|16281256|gb|BI944393.1|BI944393
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|7458604|gb|AW666054.1|AW666054
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|213587656|gb|DB971379.1|DB971379
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|213618287|gb|DB973057.1|DB973057
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|120534038|gb|EH262171.1|EH262171
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|24205256|gb|BU964509.1|BU964509
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|18039807|gb|BM308101.1|BM308101
EST:     CTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: CTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|7478542|gb|AW666307.1|AW666307
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|18041169|gb|BM309454.1|BM309454
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|37995944|gb|CF807533.1|CF807533
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|19052933|gb|BM731600.1|BM731600
EST:     TCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
EST: gi|37995965|gb|CF807554.1|CF807554
EST:     TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGG                         TGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG
genomic: TCATAACCTCAACCGTCTCGAGGCTCAGAGAAACGACCTCAATTCTAGGGgtaccctccg ... tcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaaccctcttttcttcttttcaattccttacttctcttctatttcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG
                          tccttac  putative branch site (score: 2)
       ctcttttcttcttttc  CT-rich tract
                  ttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccctccgctaaccctaaccctaaccctcttttcttcttttcaattccttacttctcttctatttcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC