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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG

Basic information

species Glycine max
transcript GLYMA13G19450.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaag-ttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG
 || |  ||| |||     | |   || | |     || |||  | | ||  |      |   | |||     ||| |  |||  |  || |    |  ||||||||||||||||||| ||||| ||||| |||||||| || || |||||||| ||  |||||
atcttattttcttcttggttgcag-agtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
gtcatcctttattccaac-ctccttcagatgtaagcataatttattct-tcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG
   ||  ||     |||| |  ||    |  | ||  |   |   |    | | | ||      | |  ||  | |  |  ||| ||  |  ||| ||  ||||||||||| ||||||| ||||| ||||| |||||||| || || |||||||||||  |||||
--tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G37500.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG
                      |    |||| |   |  | | ||| | | |  ||  ||     | |    ||  |     |  |    |  ||| ||||| |||||||| ||||| |||||||||||||||||||| ||||| || ||||| ||| | |||
---------------------gtatgtatgttattttgctatcttcctaacagttgttca-----agagctggacttaacatggagcccatctttttcagGTGATGCAAGGACTTGCTAAATCAATAGCTTGGGATGGTGAAGGTGCTACATGTCTCATCGAG

upper sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 12
--gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG
  ||||   ||   ||        |  ||   | |   |    |||| |  | |        |||  |    || |  | || |      |  | ||| ||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||||||  |||||
aagtcag--ttggctcatgaggtttagaggcttgaatttctactattatggacagcctttgggtccaatctggtcagttcttaacaaatgtccttttttcagGTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAG

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|16281999|gb|BI944782.1|BI944782
EST:     CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCG                         GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGG
genomic: CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCGgtaaagttga ... ttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGG
EST: gi|16277260|gb|BI942288.1|BI942288
EST:     CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCG                         GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACA
genomic: CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCGgtaaagttga ... ttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG
                                    agttgat  putative branch site (score: 5)
                                          ttgttctttcc  CT-rich tract
                  agaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - ctccttc
- - - - - - - - - - - - - - tgtaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcccag