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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttgttgatattggttctgtttctatctcatatacctgaatattccagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG

Basic information

species Glycine max
transcript GLYMA10G06580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
------------------------------------gtaccttgttgatattggttctgttt-ctatctcatatac---ctgaatattccagatgactgacatt-ttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
                                    || | |  ||| | || |  ||||   |||  |  | | |    |   | || ||  ||| ||   || |    ||  |  | |  ||  ||   ||||||| ||||| || |||   |||||| |||||||||||||||| ||||| || |||||||| ||| | |||||||| ||||| ||||||| |||||||
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattg-tgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgatt--gtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 7
------gtaccttgttgat-attggttctgtttctatctcatatacctgaatattccagatgactgacattttgttattg-tgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
      || | |   ||||   | |   |  ||  ||||| |||  ||    |  |    ||  |  | ||   | |  | | |  |  | ||      |||||| ||||| || ||   ||||||| |||| ||||||||||| || || |||||||| || || || |||||||| ||||| || ||||||||||||
tgtgttgtccttgactgatcgatagcctttatttgatctc-tatttctcttaagacgtactggttttctttagctgacagatataatattcttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 7
gtaccttgttgatattggttctgtttctatctcatatacctgaatattccagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
     || ||    ||  |  || ||||||  | | |   |   |||   | |||    || || | || |  |     |  | |||  | ||||||||||||||| |||| ||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || |||
--gtattattttctttcttgatgcttctattccttgtttgttgctatataatatgctgaactttcttttttatttaaactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG

upper sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 7
gtaccttgttgatattggttctgtttctatctcatatacctgaatattccagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
     || ||    ||  |  || ||||||  | | |   |   |||   | |||    || || | || |  |     |  | |||  | ||||||||||||||| |||| ||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || |||
--gtattattttctttcttgatgcttctattccttgtttgttgctatataacatgttgaactttcttttttatttaaactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG

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|8284137|gb|BE021696.1|BE021696
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTGTGGCTCTCTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|6454402|gb|AW185085.1|AW185085
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAA-TTGGGCATTAG                         TTGAAAAGGCCA-GTATTACTACATTTCTGGGCTTTT-CCTCACTGTATCT
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGG-CTTTTTCCTCACTGTATCT
EST: gi|213618065|gb|DB963698.1|DB963698
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|12689938|gb|BG156274.1|BG156274
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|17022031|gb|BM093065.1|BM093065
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATT
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATT
EST: gi|193336544|gb|FK299032.1|FK299032
EST:     GGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGC-TTTTCCTCACTGTATCTC
genomic: GGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|12690012|gb|BG156348.1|BG156348
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|151394548|gb|EV264419.1|EV264419
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|5606299|gb|AI900405.1|AI900405
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATCGGGCATTAG                         CTGCAAAGGCCAAGTATTACTACATTTCTGGCTTTTTNCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|120531830|gb|EH259963.1|EH259963
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
EST: gi|19936079|gb|BQ080713.1|BQ080713
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTAT
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTAT
EST: gi|16348521|gb|BI974116.1|BI974116
EST:     AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAG                         TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC
genomic: AAATTGCTACAAGTCTGAGCATTTGACGAGACCGGAAAATTGGGCATTAGgtaccttgtt ... ttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgaatattccagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
                gactgac  putative branch site (score: 2)
                                       tttgttttttc  putative PPT
                                       tttgttttttcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttgttgatattggttctgtttctatctcatatacctgaatattccagatgactgacattttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC