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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttgcatgtgatcttggaaccctgtaatgggatggcattttaaatttcctatttcgtaatcaaactcaccatgactttaatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG

Basic information

species Glycine max
transcript GLYMA0169S00210.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0169S00210.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 8
gtatggttgcatgtg-atcttggaaccctgtaatgggatggcattttaaatttcctatttcgtaatcaaactcaccatgactttaatccatcattc---agGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG
        | ||||  |||||  ||  |   ||| |    | |  |   | |    ||     ||| |   ||  | |  | |   | |   |||    |||| | || ||| || || ||| ||||||| || || ||||||||||||||||| ||||||||||| || || || |  ||  |  |  | ||||| || |
--------gtatgtacatcttccaaatccaaaatagctctgtagctctcagtgtgaatgca--aatgactgtctgctttccatcggttccctatttactagGTCACAGCAGTTAACCTGAAGAATGGCAGTGTGCTTGAAGCTGATATTGTTGTTGTTGGTGTTGGGGGCAGACCGCTGACTACTCTCTTTAAAGGTCAAG

upper sequence: GLYMA0169S00210.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G084881_T01 (Zea mays), 3'ss of exon 7
gtatggttgcatgtgatcttggaaccctgtaatgggatggcattttaaatttcctatttcgtaatcaaactcaccatgactttaatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG
    |  || |      |    | ||| ||  |  | ||  | |||  || |     | |  |     |||     | | ||   ||   | | ||||| |  | ||| || |||||||||||||  || || ||||| ||||||||||| || ||||||||||| || ||    ||  |  |  |||| || || |
----gtatgtaaaaccccccaaagcccagt--ttagctgtaaatttctatctgtagatccaaaggtttacttgatttaatttgtttcttgcttacagGTCACTGCAGTTAAGCTAAAGGATGGCACAGTACTTGAAGCCGATATTGTTGTTGTCGGTGTTGGAGGCAGACCATTGACTACTCTCTTCAAGGGTCAAG

upper sequence: GLYMA0169S00210.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 7
gtatggttgcatgtgatcttggaaccctgtaatgggatggcattttaaatttcctatttcgtaatcaaa-ctcaccatg-----actttaatcc-atcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG
            || || |      | | | ||   |||  | ||| | | |  ||||| | |   ||| |     |||     | || | ||  |||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||| ||||||||||| ||||| || |  ||| | ||| ||||||| ||||
------------gtaatttcttggacatctgat---atgttaattttagtatt-tatttgggagcaaaagccttttatgtagcaatttgagtcttatcattcagGTAAAGGAAGTGAAACTTAAGGATGGTAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGG

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|308098764|gb|HO760505.1|HO760505
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|21677606|gb|BQ629957.1|BQ629957
EST:     TTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|151398497|gb|EV268368.1|EV268368
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|151398847|gb|EV268718.1|EV268718
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
EST: gi|23725657|gb|BU760790.1|BU760790
EST:     TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAG                         GTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT
genomic: TCATTAAAGGAACTGTTGCTGTTGGATTCACTTCTAATTCTGATGGAGAGgtatggttgc ... catcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaaatttcctatttcgtaatcaaactcaccatgactttaatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG
                   taatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttgcatgtgatcttggaaccctgtaatgggatggcattttaaatttcctatttcgtaatcaaactcaccatgactttaatccatcattcagGTAAAAGAAGTCAAACTAAAGGATGGCAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA