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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatcaaacaaactttttactgatgaagcaaggatatattttccatgatttttaaaattgcttaatttagttcatgtacaaccaataatgtttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT

Basic information

species Glycine max
transcript GLYMA06G14960.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14960.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g02990.t01 (Vitis vinifera), 3'ss of exon 1
gaatcaaacaaactttttactgatgaagcaaggatat-attttccatgatttttaaaattgcttaatttagttcatgtacaaccaataatgtttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
   ||         ||   ||  |     | | |||| | |     |   | |||  ||   | | |||  || || || ||  | |    |||  | |||||||||||||||| || ||||||||||| |||||  | ||||||| |
-cttcttttttttcttccccttctttgttatgaatatcagtggttttctctgttattatccatgattttgctttatataaaatgacttgattttcattcagGTCATGTCAACCACTCAATTTTCTGGAAGAATCTCACCCCTGTTCAT
















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|17022337|gb|BM093371.1|BM093371
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|16348832|gb|BI974427.1|BI974427
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|7926084|gb|AW832110.1|AW832110
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAA
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAA
EST: gi|19935063|gb|BQ080093.1|BQ080093
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213597364|gb|DB962098.1|DB962098
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|6719532|gb|AW307179.1|AW307179
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298189799|gb|HO038202.1|HO038202
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|254320556|gb|GR827005.1|GR827005
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|16346801|gb|BI972396.1|BI972396
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213614908|gb|DB957002.1|DB957002
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|12774096|gb|BG239023.1|BG239023
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|14999950|gb|BI320764.1|BI320764
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213596825|gb|DB964088.1|DB964088
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTGAAG
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTGAAG
EST: gi|58021102|gb|CX707844.1|CX707844
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|151397983|gb|EV267856.1|EV267856
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAGCCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|15589944|gb|BI674560.1|BI674560
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|16278828|gb|BI943116.1|BI943116
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|16278070|gb|BI942710.1|BI942710
EST:     ATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: ATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|23728745|gb|BU762433.1|BU762433
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|23734076|gb|BU765256.1|BU765256
EST:     ATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: ATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|15000638|gb|BI321452.1|BI321452
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|209718432|gb|BW666244.1|BW666244
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|14258764|gb|BG881672.1|BG881672
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|58017804|gb|CX704546.1|CX704546
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|19346087|gb|BM890967.1|BM890967
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgttcgattcc ... tttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttaaaattgcttaatttagttcatgtacaaccaataatgtttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
              gcttaat  putative branch site (score: 4)
     tttaaaattgcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatcaaacaaactttttactgatgaagcaaggatatattttccatgatttttaaaattgcttaatttagttcatgtacaaccaataatgtttattgcagGTCATGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT

- - -aaacaaa
- - - - - - - - - actgatg
- - - - - - - - - - - - - - - - - - - - -tccatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccaa