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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttacttttcacgctgttgaacagaagcattttttcagtgtatttaaatgcatgcacctagttaacttctgcatatgcttcgtttttttggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC

Basic information

species Zea mays
transcript GRMZM2G062024_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062024_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
---agtttacttttcacgctgttgaacagaagcattttttcagtgt----atttaaatgcatgcacctagttaacttctgcatatgcttcgtttttttggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC
   |   | ||  |||    |       | || || | || | | |    ||    ||      | ||| |||| ||||        ||  || || |   ||| |||| || ||||| | ||||||||||||    || || |||  ||||||||||||  |||||||  | || |||||| |||||||||||||||| |||||||
taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttct-------tttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC
















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|32840593|gb|CD980274.1|CD980274
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840289|gb|CD979970.1|CD979970
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840250|gb|CD979931.1|CD979931
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840295|gb|CD979976.1|CD979976
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|211124332|gb|FL444268.1|FL444268
EST:     TTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: TTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|60350509|gb|DN217482.1|DN217482
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840308|gb|CD979989.1|CD979989
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|5108252|gb|AI739965.1|AI739965
EST:     GTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840674|gb|CD980355.1|CD980355
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|29545180|gb|CB605358.1|CB605358
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840071|gb|CD979752.1|CD979752
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCA
EST: gi|32840128|gb|CD979809.1|CD979809
EST:     GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAG                         GCACCCTGGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGC
genomic: GGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCA-CCT-GTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 88

TGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 92

TGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 112

TGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 128

TGTAGGGGCAATATTCTGCTTTGGTGCTTTTTGTTTCAAGAGCCTTTATGGGTTCATACCCTCCTTTGCAGTTGGGGAGCTTTCAGTGTTCGCAACTCAGgtaattgctt ... tggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgcatgcacctagttaacttctgcatatgcttcgtttttttggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC
                agttaac  putative branch site (score: 128)
                                tgcttcgttttttt  putative PPT
                                       ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttacttttcacgctgttgaacagaagcattttttcagtgtatttaaatgcatgcacctagttaacttctgcatatgcttcgtttttttggtttgcagGCACCTGTAAATTTTGTATGCCTTCACGCCGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGC

- - - - - - - gctgttg
- - - - - - - - - - - -cagaagc
- - - - - - - - - - - - - - - - - - - - tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctgc