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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

Basic information

species Glycine max
transcript GLYMA15G10370.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
----gtcagtat-ttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatg-gttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
    |    ||| | ||| | ||| |   || | ||     ||  |||| | |    ||  | |  |||| ||| |||| ||  ||     |||||| ||||||| |||  |||| ||||| || ||||| |||||||| ||||| ||||||||||||||||||||||||||||| ||||||
gtatgctgttatgtgcaaattgttttcttctgaaccc----atgaatatgtatgttgaatatttagtgttaatgtgttgatgtctt-----cagGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggt--tggtgcttt--tacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
           | ||  || |  | || |  || |  ||| |   | |||  || || |   ||| | |||  ||||  |||  |   ||||||| || ||||| ||  |||| || || |||||||| ||||| ||||||||||||||||||||||||||||| || || || ||||||
---------gtatgtccttttcaaatc-gtaattt--tttctcattctac--aatttgtgaagttaaaggttatggttatttggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
       | | |     |  |  |||      | |   |||       |   ||  || |   |   |  ||  ||    | ||   |||| ||||||| |||  |||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||||
------gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctcca---gGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
gtcagtatttcaagtagttatg---gactcagccatctgatttatatctgtacca--aaattattttgttgatggt--tggtgcttttacaa---cagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
    ||||   |  | ||||||    | | ||   | |   ||||| |   | ||  ||   ||     | ||| |  | || ||| |       |||||| || |||| |||  |||| |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||| ||||||
----gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
         | | |   || | |  ||     |   ||||||   |||       |     |  ||| ||| ||||  || |   ||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || || || |||
--------gtaaggctctttttgtgtccattgt--aatttatgagtgttttcttttatgcctaatga-ggtgggtggatt-atggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
|| ||| | |||  |  || |  |||      | |||  | | |||  ||         ||||  || |  |||   | ||    ||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||
gtaagtctctca--tcattgtccactgtagtttatgaactttctcttcacg--------tttgacga-gtctggca-tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattat-tttgttgat--ggttggtgcttttacaaca-----gGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
|| || |||||      || |   ||    | | |    |      | |     ||  | |||    ||  ||||| |   ||||   ||     ||||||| |||||||| ||||| || || |||||||||||| |||||||||||||||||||||||||||| || ||||| || || |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
                            |  ||   ||    || ||| |  |   |    ||||     || |   || | |  |||||| || ||||| || ||||| || || ||||| || ||| ||||||| || || |||||||||||||||||||||||||| ||  ||
----------------------------gtaat--aataatgatttgttctgag--tggcatgttt----ttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtcagtatttcaagtagttatggactcagccatctgatttat-atctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
                                |   | | || || ||| |  |   |    ||||     || |   || | |  |||||| || ||||| || ||||| || || ||||| || ||| ||||||| || || |||||||||||||||||||||||||| ||  ||
-------------------------------gtaatagtaatgatttgttctgag--tggcatgtt-----ttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

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|6069767|gb|AW099383.1|AW099383
EST:     GGTATTAATCTTGCTACTGCTGATGTTGTCATTCTGTACGATAGTGACTG                         GAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCA
genomic: GGTATTAATCTTGCTACTGCTGATGTTGTCATTCTGTACGATAGTGACTGgtcagtattt ... tttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
                            tgttgat  putative branch site (score: 4)
                                         tgctttt  putative PPT
                  aaaattattttgttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT