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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggcataaatttactccttttagttgtttcatttctctgtcttatatttcatggcatatggatttatttctctgtcttaatttttttccttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATGAACAGGGATGGATCTGAGTGTCCCTTTGATGTGAAAGACATCCAACGGT

Basic information

species Glycine max
transcript GLYMA09G34650.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34650.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g01160.t01 (Vitis vinifera), 3'ss of exon 1
-ctggcataaatttactccttttagttgtttcatttctctgtcttatatttcatggcatatggatttatttctctgtcttaatttttttccttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATGAACAGGGATGGATCTGAGTGTCCCTTTGATGTGAAAGACATCCAACGGT-----------
  | || ||| | | |     |   || ||   ||  | | | || | | |||  || | |  |  |||   ||| |   |||| |  || || ||  | |  || | ||       | ||| | ||||||||||| || ||||||||| |||||  ||||| |||||| ||||||||||||| | | ||||| ||    |           
ctttgcttaattatgc---catagattattaacttcttttttgttctttatcaatgcgtctaaaagtat---tctatgcaaattct--tctttcttctttgttgatagTT----GAGAGAAGGAAGCAATGGACTTTTTCTTTAAGGGACTGAACGCGGATGCATCTGAATGTCCCTTTGATGAGCAGGACATTCAGAAATGCCCATTCTTA
















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|151395813|gb|EV265690.1|EV265690
EST:     GTGTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTAC-                         --GAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GTGTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|209720586|gb|BW654439.1|BW654439
EST:     GTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACG                         AAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|151400423|gb|EV270237.1|EV270237
EST:     GTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTAC-                         --GAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|298167526|gb|HO012789.1|HO012789
EST:     CAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACG                         AAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: CAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|38192748|gb|CF921954.1|CF921954
EST:     GTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTAC-                         --GAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GTCTGTGGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|14999869|gb|BI320683.1|BI320683
EST:     GGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACG                         AAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GGCAGCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
EST: gi|15288136|gb|BI472027.1|BI472027
EST:     GCCACACGTCTTGGCAGTTCTCTTCTCTGATTAC-                         --GAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG
genomic: GCCACACGTCTTGGCAGTTCTCTTCTCTGATTACGgtacttcttc ... ttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcatggcatatggatttatttctctgtcttaatttttttccttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATGAACAGGGATGGATCTGAGTGTCCCTTTGATGTGAAAGACATCCAACGGT
                              tcttaat  putative branch site (score: 3)
                  tttatttctctgtctt  CT-rich tract
                            tgtcttaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggcataaatttactccttttagttgtttcatttctctgtcttatatttcatggcatatggatttatttctctgtcttaatttttttccttgtttctagAAGAAATTTTTTCAGCAAAAGCAGGCAATGGACTTCTTTTTTAAGGGAATGAACAGGGATGGATCTGAGTGTCCCTTTGATGTGAAAGACATCCAACGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - -ctgtctt
- - - - - - - - - - - - - - - - - - - - - - - - - catggca