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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaagaacggagggagtatatacctagtataaagcttatgcaatacagaagattgatcacattatgttgtaaagctgaaagactcatgactgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG

Basic information

species Zea mays
transcript GRMZM2G037698_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037698_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 14
aaaaagaacggagggagtatatacctag----tataaagcttatgcaatacagaagat-tgatcacattatgttgtaaagctgaaagactcatgact--gtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG
                |||| | |  |     |  ||  || |     |   | | || | ||  | | |  || || |  ||| |    |     |  |  |  ||||| ||||||||||| |||||||||   |||||||||||  ||||||| ||||||||||| || || ||||
----------------gtattttctcaaaacctgcaagtctgaccttttggtgcaaatgttataccgtaaacttttatatttgatacctcctctgtttggccttcagGGTTTACCAAGTAGCAAATGTTAAGCTTGAATGGAATCTTGTCAAGACCTTACCAGATTTGTCAGGCACAG
















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|6022161|gb|AW067089.1|AW067089
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|32908360|gb|CF013173.1|CF013173
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|5055844|gb|AI734731.1|AI734731
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|32934237|gb|CF039049.1|CF039049
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|20811259|gb|BQ295737.1|BQ295737
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|24764727|gb|CA399890.1|CA399890
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|211335935|gb|FL468899.1|FL468899
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|33090853|gb|CF050847.1|CF050847
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|32933281|gb|CF038093.1|CF038093
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|148987119|gb|EE030947.2|EE030947
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|8577012|gb|BE129649.1|BE129649
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|78024591|gb|DV492978.1|DV492978
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|32837457|gb|CD977135.1|CD977135
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAAATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|60341462|gb|DN208435.1|DN208435
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|5607968|gb|AI901635.1|AI901635
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|32936163|gb|CF040975.1|CF040975
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
EST: gi|33103734|gb|CF063694.1|CF063694
EST:     GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG                         GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT
genomic: GAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATT

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: 256

TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 106

TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAGgtatgttcta ... ctgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagaagattgatcacattatgttgtaaagctgaaagactcatgactgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG
      gattgat  putative branch site (score: 106)
                attatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaagaacggagggagtatatacctagtataaagcttatgcaatacagaagattgatcacattatgttgtaaagctgaaagactcatgactgtgtctagGGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG

-aaaagaa
- - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa