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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcccttttctattctctctctctctctctctcttttttcctttcttcattcttccattctattctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGAACTTCAAGAAATTCAGGACAACATTCGAAGTCGGAGGAACAAAATCTTC

Basic information

species Glycine max
transcript GLYMA12G00600.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------gtcccttttctattctctctctctctctctctcttttttcctttc-ttcattcttccattctattctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGAACTTCAAGAAATTCAGGACAACATTCGAAGTCGGAGGAACAAAATCTTC
                         ||    | |  | |   |     |   | |   |    |   ||  ||  | |     || |  | |    |||| || || || |||||||| || ||||| ||||||||||||||||| |||||||| ||||||||||| || || |||||||||||| | |||||||| |||
tattaaaaaaaaatgataaatagtcgtgttgtctgcagtggatgagcttaaatgtggttcagctgtgttgatttgtccacttgttatgctttgaatgcagCTTTTGTATTATTGAAGGACCTGAAACAGTACAGGATTTTGCCAAAATGGAACTGCAAGAAATTCAAGATAATATTCGAAGTCGGCGAAACAAAATTTTC
















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|120491443|gb|EH219610.1|EH219610
EST:     G-CTCTTCTTTTGCACCCTCTCTTGACTCCTACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|6566524|gb|AW234167.1|AW234167
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCACTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|19269603|gb|BM885859.1|BM885859
EST:     CGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: CGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|18038871|gb|BM307165.1|BM307165
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|9819295|gb|BE554808.1|BE554808
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|13479753|gb|BG509096.1|BG509096
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCACTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|33389909|gb|CA853116.1|CA853116
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCACTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|298167160|gb|HO010599.1|HO010599
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|13480083|gb|BG509426.1|BG509426
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|33389270|gb|CA852477.1|CA852477
EST:     ACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCACTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: ACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|193611684|gb|FK565341.1|FK565341
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCACTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|12773323|gb|BG238250.1|BG238250
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|4306078|gb|AI443853.1|AI443853
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
EST: gi|12689436|gb|BG155833.1|BG155833
EST:     GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGG                         ATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA
genomic: GACTCTTCTTTTGCACCCTCTCTTGACTCCGACAAAACCGCCTCTGCTGGgtcccttttc ... ctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctctctcttttttcctttcttcattcttccattctattctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGAACTTCAAGAAATTCAGGACAACATTCGAAGTCGGAGGAACAAAATCTTC
       ctctctcttttttcct  CT-rich tract
            tctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcccttttctattctctctctctctctctctcttttttcctttcttcattcttccattctattctatccgcagATTCTGCATCATTGAAGGCCCAGAAACGGTACAGGATTTTGCCAAGATGGAACTTCAAGAAATTCAGGACAACATTCGAAGTCGGAGGAACAAAATCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA