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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgctcttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT

Basic information

species Glycine max
transcript GLYMA19G37930.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 3
tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgct-cttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT-
                      | | |   |  ||   |  | || ||    | |   |  | | |  ||| ||| |   ||     ||||||||||| || || |||||| | ||| |||||||||||||||||||  |||| || |||||||||||||||||||| ||| | || |  |||||| | |        ||  
---------------------gtttatgatttgtgcacaacatttcctcctctctacttattacctcctttcactaccttacggag-gcttctcctgt-agGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTAC-ATCTTGAATAACG

upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G163996_T01 (Zea mays), 3'ss of exon 3
tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgctcttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT---
            | |   |  | || | |    |    | |  ||| ||||    || ||  | |   ||      ||||   |   ||||   |  ||| || || ||| | ||| | || |||||||||||||| |||||||| || ||||| ||||||||||| ||||| || |  || ||  |   | |||||      
-----------gtatgcctgctactctactacgtagttatt-tttgttttgccc-cactgtccatcagtttgaagttacaaactaaacttcctgttgcagGTCCGAGTTTGTGTTCATAAACCCAAATTCCAAAGGGCAGTGTGGCTGCGGTGAGTCTTTCATGACTACAGGCAGCAAAGGGTCGAC---GTCATGAGGCGTT

upper sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g03400.t01 (Vitis vinifera), 3'ss of exon 2
---tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgctcttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT
   |  | ||||     |  |  |  |     | ||  |   |       |   ||         | |  ||||| |  |    ||      |||   | ||| || || || || ||  |||||||||| || ||||| ||||||||||||||||||||||||||||||||||| | |  |||| || |||||        |
tctttctttgttagagataatcatggccagaaccaaaataggcacaccattaacttgattaaaacccttctttaatttgt---tttcccttgtctttgggcagGTCTGAGTTCATATTTATCAATCCAAACTCTAAAGGGCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGCAATCCTGGAGCTGCTAAGTAGGTTGGT

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|31311334|gb|CD396537.1|CD396537
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAG                         ATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
EST: gi|23729629|gb|BU762912.1|BU762912
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAG                         ATCGGAATTTATTTTCGTCAATCCAAAATCCAAATTCCAAAGGTCAGTGTG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAA-T-----T-CCAAAGGTCAGTGTG
EST: gi|58018339|gb|CX705081.1|CX705081
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAA                         ATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
EST: gi|31308109|gb|CD393312.1|CD393312
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAG                         ATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
EST: gi|7233513|gb|AW568858.1|AW568858
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAG                         ATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGG
EST: gi|213617107|gb|DB963580.1|DB963580
EST:     CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAG                         ATCGGAATTTATTTTCGTCAATCCAAAATCCAAATTCCAAAGGTCAGTGTG
genomic: CTTATGCATGTCATTGGAACTAAAATGGATTTTGTAGATGACAAACTAAGgtaaatgttt ... ctcctgtcagATCGGAATTTATTTTCGTCAATCCAAA-T-----T-CCAAAGGTCAGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgttttcagtgctcttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT
                     ttttaac  putative branch site (score: 2)
                           ctcctacactttttgc  CT-rich tract
                tcttattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgctcttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
-catctgt
- - - - - - - - - - - - - - - - -tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctac