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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC

Basic information

species Glycine max
transcript GLYMA16G09330.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
                || | | | |      ||     || | |  | |  |   ||    | | || |  | || ||| |     |     |  |   ||||||| || || ||||||||||| ||||  || ||||||||||| || || || || ||||||||||||||||| ||  ||||  |||| |  ||| | |
--------------gtaatatcgtgaggcctctg-----atgtttcctaattactgttacctagtcttaagat-gttaacatatctctctcctttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaat---tatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
                |||   |     | ||| ||||   |||  | |      |||| | |||    |  |  | |    |   ||   | |  |  |   |||| ||||| || ||||||||||| ||||  ||||| |||||||||||||| || ||||||||||| ||||| || ||  ||||  |||| |  ||| |||
--------------gtaaattttctgctttcttatttcttgatccat-gccccctattgctgatttcatacttaattataggtgtgatgtgtttcttttttgcagGAGTTTAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAACAAGGCTTCCCAATGAAGCAAGGAGTTCTGACTTCTGGTCGTGTCCGCCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgagga--gcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
|||  || ||  |||    || |   | | |||| | || |  || |||  ||   |||   ||| ||| | | |  |    ||     || |||       |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  |||||| |||| |||
gtaaactttg-ggat---gactt---atttcttgatcca-tgactcttgctgatttcatacttaaatataggtgtgatatgtttctttgttttgc-------agGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T08 (Zea mays), 3'ss of exon 3
-------gt-atgctctgta-gatcaaaaccttcaaat-acttgtttcaatatct----tttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
       || ||||||||   ||   |||| ||    | |||| ||||   |||      |   |  |  || ||| |||   || | |       ||   || |     |   |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  |||||| |||| |||
gtcagtggtgatgctctgggtgaggtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtg-tgatatgtttctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T05 (Zea mays), 3'ss of exon 3
--gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
  |  ||   |  |  |           | | |||| | || |  || |||  ||   || ||| |||   || | |       ||   || |     |   |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  |||||| |||| |||
ctgggtgaggtaaactttggggtgacttatttcttgatcca-tgactcttgctgat--ttcatacttaaaaatataggtg-tgatatgtttctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
gtatgctctgtagatcaaaaccttcaaat-acttgtttcaatatcttttgaggagcattgata--attattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
    |   || |  |  |||| ||   || |||| ||||   |||  | ||       ||||   ||  || |   |        ||   |  |     |   |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  ||||||  ||| |||
----gagttgaatttacaaactttgggatgacttatttcttgatccat-gactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGGTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGCCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
|||  || ||  |      || |   | | |||| | || |  || |||  ||   || ||| |||   || | |       ||   || |     |   |||| || || || ||||||||||| ||||  ||||| |||||||| ||||| || ||||||||||| |||||  | ||  ||||  |||||| |||| |||
gtaaactttggggt----gactt---atttcttgatcca-tgactcttgctgat--ttcatacttaaaaatataggtg-tgatatgtttctttgttttgcagGAGTTCAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgagg--agcattgataattat-tgatcttgtcaacttta-aaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
        |  ||||   |   |||  |   ||| |  |||   | |  ||   ||||||   ||  |  ||||  |||    ||||  |||| |  |  |   |||| || |||||||| || ||||| ||||  |||||||| || || ||||| || |||||||||||||||||  | || || ||| ||||||  |||||||
-------gtacagattccatttttcttac-tttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgagg--agcattgataattat-tgatcttgtcaacttta-aaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
        |  ||||   |   |||  |   ||| |  |||   | |  ||   ||||||   ||  |  ||||  |||    ||||  |||| |  |  |   |||| || |||||||| || ||||| ||||  |||||||| || || ||||| || |||||||||||||||||  | || || ||| ||||||  |||||||
-----aggtacagattccatttttcttac-tttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttg--tttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
||| ||  |    | ||      |  ||| |     ||  | ||||     ||    ||  ||||   ||  | ||||    ||     || ||    | | |||||||||| || ||||| ||||||||||  || || |||||||| ||||| || |||||||||||||||||| |||| |||||  |||||  ||| ||||
gtaagcatt---taccattgttatgcaatgccaaaattctactatcagactagatttat--ataacatttatttttgtttgttt---gtttgtg----tgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
              |   |   |   | || |  | | |  ||   |||       ||   ||| ||| || |  |  |  ||||   | |     | | |||| || || || ||||| |||||||| |  || || |||||||| ||||| |||||||||||||||||||| || || || ||| | || || ||| |||
-------------gtatgattttgttactattcttcttaggataacttgccctttgttaggaatgatttat-tgatgtatcttaagcgtgt----ttgacagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC

upper sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
||||||  | |         |   ||  || || | ||| |||  |||||              || | ||| |   ||   |   ||  ||||  | | |||| || || || ||||| ||||| ||||  |||||||||||||| ||||| ||||| |||||||||||||| || || |||||| |||||  ||||||||
gtatgccttttctgctctt-ctcccacttatttatctca-tattgtttga------------tctactaatcatacaaaacatgtcatc-tgct--tcacagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC
                 tattgat  putative branch site (score: 3)
                                 tttaaaattatgctac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctgtagatcaaaaccttcaaatacttgtttcaatatcttttgaggagcattgataattattgatcttgtcaactttaaaattatgctactaatagGAATTTAAAGGATATGTCTTCAAAATCACTGGTGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTAACACCTGGCTGTGTTCATCTTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC