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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG

Basic information

species Glycine max
transcript GLYMA08G09170.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 7
----agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
    |  |   ||   |  |  |     ||||||  || |    |||| |  | |    || |  ||| ||   |  |||   |  ||     ||  || |||||||||||||||||||||||| ||||||||||| ||| | |
gtgcaattgtgatacctaca-aatattgttttga--tgctgcctatttaaaatgttaaatgatggcat-tctttttttttttcacatgctctgttcgaaaccagGTAGCAAAGGCTCCTGATGGCAATGGTGGAGTTTATGCTG

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------------agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggt--tacatgtccggtggt-ttaata------tttgaaactttt-----aaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
                                                                    | |    |||    |||     ||   |  |    || | ||  ||    | |||   |  | | || |   |||  |||||       |||| ||| ||      ||| | ||||||||| |||||||||||| ||||||||||||||| | |
gtttttaccttgctttatttatatttttttatttcatctcccattcttccatcattccgttgcaagtgaaccagcattggactatctaatcaaaatacaagtattgtgataataaacttgcttgaatggtgcttgccttctggggttaatgacatcttttgcaacattctgttgaaaactagGTAGCAAGGGCTCCTGATGGCAATGGTGGAGTGTATGCTG

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 6
agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaacttt---taaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
   |   |||||   |    |   |||| |||   |  | |    |   | ||    | ||  | |  ||   | |  |  |  |  || |   | || |||||||||||||||||||||||| || |||||||| ||| | |
--ttttcattttgacagagtcttttttttaatatatactgagcaaaaaaaaacaaatgctaagt-tgtggcattcttgttgtccatgctgtggatgaaaccagGTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 7
--agctcctatttttttatgaccccatt--ttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaactt-ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
   | |  | |   ||| |  || | ||   |||||| |||| ||||| |  | |  | ||   | ||     ||||||  |||| |  || || ||||||||||||||| |||||||| ||||| ||||| ||||| |||||||
taggattatttccatttttaccctccttagctgaatt-ttttaaatttcaaatttgttctgaaaatata----gtggttacatatatctaatttcttaaagccagGTAGCTAAGGCTCCAGATGGAAATGGAGGAGTATATTCAG

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|6454569|gb|AW185252.1|AW185252
EST:     TCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGG                         GTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
genomic: TCCCTTGTGTTTCCAAGGATGGCAGATTTATTATGGAGACTCCATACAGGgtatactctc ... ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
EST: gi|10235209|gb|BE804156.1|BE804156
EST:     CCCTTGTGTTTCCAAGGGATGG-AGATTTATTATGGAGACTTCATACATG                         GTAGCCAAAG-CTCCTGATGGGGAATGGTGGA-TGTTTTCAG
genomic: CCCTTGTGTTTCCAAGG-ATGGCAGATTTATTATGGAGACTCCATACAGGgtatactctc ... ttaaagccagGTAGC-AAAGGCTCCTGATGGG-AATGGTGGAGTGTATTCAG
EST: gi|254329705|gb|GR839258.1|GR839258
EST:     TCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGG                         GTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
genomic: TCCCTTGTGTTTCCAAGGATGGCAGATTTATTATGGAGACTCCATACAGGgtatactctc ... ttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatactttggttacatgtccggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG
                           gtttaat  putative branch site (score: 4)
                                          ctttt  putative PPT
                            tttaatatttgaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctcctatttttttatgaccccattttgaattgtttttaattttatgtatactttggttacatgtccggtggtttaatatttgaaacttttaaagccagGTAGCAAAGGCTCCTGATGGGAATGGTGGAGTGTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG