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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataagaaaatacatacagatattttgaagttctctccatgctttttaaagcttgtaatcaattttgtattattgccttatgatattttttcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC

Basic information

species Zea mays
transcript GRMZM2G381933_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381933_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 12
aataagaaaatacatacagatattttgaagttctctccatgctttttaaagcttgtaatcaattttgtattattgccttat-gatattt--tttcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC
   | |||   ||  | |    |  || |         | |    |   |  |||    |  |||| |    ||| ||||| ||||  |  |||||||||||||||||||| | ||||||  |   ||| |||||||| ||| ||||||| || || || ||||||| |||||||||||  || || ||||| ||| || || 
---aggaagtgacgaaaatgcctactgtaaactatgaaaagagagtcggaaattgcttcctttttttttcatttgtcttatagataactggtttcttatgcagATCAAATGCAAAAATGTGGTCATTCTCGCTGCAACTAATGTGGATGAGCTTGAAACGGAGTGGGGTTGTCTTCTAGACACACAAGAGAGCGGTTTAGTGA
















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|60359540|gb|DN226513.1|DN226513
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|60396268|gb|DN229137.1|DN229137
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|71767359|gb|DR965296.1|DR965296
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|60351624|gb|DN218597.1|DN218597
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|60394781|gb|DN227651.1|DN227651
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|34391288|gb|CF384516.1|CF384516
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
EST: gi|74242521|gb|DT650435.1|DT650435
EST:     CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG                         ATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA
genomic: CAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTA

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: 119

ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 173

ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTGgtatgttctt ... tcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagcttgtaatcaattttgtattattgccttatgatattttttcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC
                                      tattttttctt  CT-rich tract
       ttgtaatcaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataagaaaatacatacagatattttgaagttctctccatgctttttaaagcttgtaatcaattttgtattattgccttatgatattttttcttatgcagATCAAATGTAGAAATGTCATTGCTCTTGCTGCAACCAATATGGATGAACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- -aagaaaa
- - - - - -acataca
- - - - - - - - - - - - - - - - - ctccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctta