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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG

Basic information

species Zea mays
transcript GRMZM2G103812_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
-----tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
||| || || | || | ||| |||| || | | | ||| |||| | | | | | || || || | ||||||||||||||||||||||||| ||||||||||| ||||| | ||||| || ||||| |||||||| ||||||||||| ||||||||||| ||||||||
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataacca-----tagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------tgcagatgtatggtaaaattgcttg-aca-tgtgaaaaacagacagattc-attatgatgatctcagtgtctttattacttattaagtttctgctacatg-cagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
|| | | ||| ||| ||| ||| |||| | ||| | | | ||| | | | | || | || || | | || | || ||||| ||| || ||||||| |||| ||| ||||| ||||||||||| ||||| || ||||||||||||||| | |||||||||||||| || |||
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 3
tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtcttta--ttacttattaagt--ttctgctacatg-cagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
| | |||| | ||| | || | || || | | | | | ||| | |||| | || | || || | | | || || || || ||| ||||| || ||||| || ||||| | ||||| || || ||||||||||| || || |||||||| ||||||||||| ||||||||||| ||||||||
-gaacatgtccag-ggaatggtttta---gtataacatgagccaacctctgacattgagcacagtattttaagtttgattttccactccttttgatatatatcagATGGGAGAAACCAGGGCATAGTCCGTCTTTTGGCTACGATTTCTGGTACCAACCCCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ11187 (Selaginella moellendorffii), 3'ss of exon 3
tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctg---ctac-atgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
| || || | || | | || | | ||| | | || || || | ||| | || |||||||| | ||| |||||||||| ||||| || ||||| ||||| || ||||| ||||| |||||||||||| || ||||| || || | |||
-------------------------------gtaagttctcgtgagttcttgtctt--tcacgccattttttgtcactgttgagctttggatcttacgacttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG

upper sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ15679 (Selaginella moellendorffii), 3'ss of exon 3
tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
|||| | | ||| | | | | | | | | | | || |||| | | | | | || || | || |||||||| | ||| |||||||||| ||||| || ||||| ||||| || ||||| ||||| |||||||||||| || ||||| || || | |||
------------gtaagttctcgtgagttctcgtgagt--tcttgtcgttcacgccattttttgtcacttt-tgagctttggatcttatg----acttagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG

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|149083207|gb|EE172484.2|EE172484
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|211184168|gb|FL127369.1|FL127369
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACT
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACT
EST: gi|38502601|gb|CF972461.1|CF972461
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|5268463|gb|AI770427.1|AI770427
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31355194|gb|CD439551.1|CD439551
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCTGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31350247|gb|CD434604.1|CD434604
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31354133|gb|CD438490.1|CD438490
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|60355186|gb|DN222159.1|DN222159
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31349415|gb|CD433772.1|CD433772
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31360531|gb|CD444888.1|CD444888
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31355476|gb|CD439833.1|CD439833
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|31356060|gb|CD440417.1|CD440417
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|29167955|gb|CB411215.1|CB411215
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|14701286|gb|BI233704.1|BI233704
EST:     GAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|14701287|gb|BI233705.1|BI233705
EST:     TTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: TTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
EST: gi|67031397|gb|CO460146.1|CO460146
EST:     GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA
genomic: GCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCA

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: 404

CGTCTGGCGACATTATGATTTCTTGCCTTGGGGACAAGGAGGGGAATGCAGCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2048

CGTCTGGCGACATTATGATTTCTTGCCTTGGGGACAAGGAGGGGAATGCAGCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1031

CGTCTGGCGACATTATGATTTCTTGCCTTGGGGACAAGGAGGGGAATGCAGCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 570

CGTCTGGCGACATTATGATTTCTTGCCTTGGGGACAAGGAGGGGAATGCAGCTGGCAATGGCTTCCTGCTGTTGGATTCAGAGTTTAATGTCAAAGGACGgtaagttctt ... ctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG
                                       tttctgct  CT-rich tract
 tctttattacttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-gcagatg
- - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat