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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtgatcatgcgatgtattttcttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG

Basic information

species Zea mays
transcript GRMZM2G173989_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 4
gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtga---tcatgcgatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
        | | || || |      |||||    |||| ||     |  |  ||    ||||  ||| |||| |     |||| ||||  | | ||  || |||||||||||| ||||| || ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||||| |||||||| || || |||||||||
--------ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG

upper sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 5
gggctttgcaagaagctagacgactgtttttatgttaattg---tattttgcctgtgatcatgcgatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
        | | || || |      |||||    |||| ||    ||  ||       ||||  ||| |||| |     |||| ||||  | | ||  || |||||||||||| ||||| || ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||||| |||||||| || || |||||||||
--------ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG

upper sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g08490.t01 (Vitis vinifera), 3'ss of exon 4
gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtgatcatgcgatgtattttctt---ttctgaaatagct---ttggtta-------ttacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
             |  ||||  |  ||||   |   ||  |||  |    | | |  |    || || | ||      ||| ||||   |   || |||        || ||||| ||| | || ||||| || || |||   ||||| ||||| || || ||| |||||||||| || ||||||||||| ||||||||||| |||
------------tatttagagcatcgtttacttaccaaaagtaaataattt-taaatactatatttactctcacaaactctaaaatgattacctttgttcccatcatttgcagAATTTTCTTGTGGACATCAAAGGACCTGCATTGGCATTTCTGCCTGTGCTTGCATTTGAAGGAGGAACAAGGAGAAATATACCCAAGTTTGAG

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|110532784|gb|EE036964.1|EE036964
EST:     GGTATTGTGGTGGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: GGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|211405711|gb|FL168805.1|FL168805
EST:     GTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: GTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|110193156|gb|EC875054.1|EC875054
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|78107144|gb|DV525562.1|DV525562
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|149086168|gb|EE175709.2|EE175709
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|76290159|gb|DV029727.1|DV029727
EST:     ACCAACCCAGAC                         AAC-TTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: ACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|76016002|gb|DT943172.1|DT943172
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|78122587|gb|DV540971.1|DV540971
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|60358632|gb|DN225605.1|DN225605
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
EST: gi|32858453|gb|CD998134.1|CD998134
EST:     CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC                         AACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT
genomic: CTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

TATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

TATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

TATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 51

TATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACgtaagtatac ... gttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctgtgatcatgcgatgtattttcttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
                 atgtattttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtgatcatgcgatgtattttcttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- -ctttgca
- - - - - - - - - - - actgttt
- - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - - tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcga