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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC

Basic information

species Zea mays
transcript GRMZM5G819212_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g47930.1 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttg--aaatttagttgtttttttccgtatacttctcca-aacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                          ||  |  |  ||  |    |  ||| ||   | |||||||| |  ||   ||  | ||| |  |    ||| | |||| ||||| |  | ||||| | || |||||||||||| || || ||||||||| ||||||||||||||||||||||||||||| 
------------------------------------------------------------------------------------------gggctttattttaatggaagacaaacttgtgtttttttttctgagtaaaactatagaactgatcgatatgagtgcattttgtgctttatttgattttaagAAGAGGAAGTCAATGACTTGGGAGTCAATGTGGCACTATCCATGCTAAAATTTTACAAAA

upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g15970.3 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttga-aatttagttgtttttttccgtatacttctcca-aacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                         |||  |  |  ||  |    || ||  | ||  |||||||| |  ||   ||  | ||| |  |     || | |||| ||||  | |||||||| | || |||||||||||| || || ||||||||  ||||||||||||||||||||||||||||| 
----------------------------------------------------------------------------------------ttgggctttattttaatggaagacaaacttgtgttttttttctgagtaaaactatagaactgatcgatacgagtgcattttgtgttt-ttgtgattttaagAAGAGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAA

upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g15970.4 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctcca-aacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                          || || |   |  |       ||  | ||  |||||||| |  ||   ||  | ||| |  |     || | |||| ||||  | |||||||| | || |||||||||||| || || ||||||||  ||||||||||||||||||||||||||||| 
------------------------------------------------------------------------------------------ggctttattttaatggaagacaaacttgtgttttttttctgagtaaaactatagaactgatcgatacgagtgcattttgtgttt-ttgtgattttaagaagAGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAA

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|211094336|gb|FL133038.1|FL133038
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|87156647|gb|DY401436.1|DY401436
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|22521085|gb|BU079896.1|BU079896
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|26557890|gb|CA830125.1|CA830125
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|21809855|gb|BQ668173.1|BQ668173
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|21331586|gb|BQ486967.1|BQ486967
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|87156978|gb|DY401767.1|DY401767
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|21389849|gb|BQ527898.1|BQ527898
EST:     TGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: TGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
EST: gi|26559014|gb|CA831249.1|CA831249
EST:     GAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         GCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA
genomic: GAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCA

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: 46 (upstream exon), 45 (downstream exon)
Score: 11

TTTCTTTCGGTGCTTCGTGCCACAAGTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 10

TTTCTTTCGGTGCTTCGTGCCACAAGTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 5

TTTCTTTCGGTGCTTCGTGCCACAAGTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 11

TTTCTTTCGGTGCTTCGTGCCACAAGTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... ctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacattgtttcttgaaatttagttgtttttttccgtatacttctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                            tttttttccgtatact  CT-rich tract
              ttgaaatttagttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctccaaacagGCCTGCTTGACTACATTATGTGCATATTGTGATTCTCAGCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC

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