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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttcccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg...

Basic information

species Zea mays
transcript GRMZM2G031802_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 1
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgta-cgcccttctcttc----ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg
|   |||||||||||| ||||||||| || ||||||||||||||||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||||| ||| |  | |  |    ||   ||    |  |||    |  |  || ||| | |    ||    ||  | | || || |||   |  || |||        
GCGGCGGAGATGAACGCGTTCCGGCTAGCCGGGGACATGACCCACCTCCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgccacgccgcggacccaaatctttgctgctgctgccgcgtgtatgatcc-actctcctcgcctgttcg-gcagctattctgctttacttttcttt---

upper sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g28340.2 (Oryza sativa), 5'ss of exon 1
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgta-cgcccttctcttc----ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg--------------------------------------------
                                               |||||||||||| ||||| ||||| |||||||| |||||||||||||||||||||| ||| |  | |  |    ||   ||    |  |||    |  |  || ||| | |    ||    ||  | | || || |||   |  || |||     ||                                             
-----------------------------------------------CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatcc-actctcctcgcctgttcg-gcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt

upper sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttc--ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg
| | | | ||||||  | ||||||||    || ||||||||||| ||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| |||| |                ||| ||   |  | |  |  | |||       ||| || |        |||||| |                         
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagagagaaaattttcttcgattcttttgatttcgtgctg----cttagaaatct-------ttgcgcag-------------------------

upper sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ30337 (Selaginella moellendorffii), 5'ss of exon 1
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttc--ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg
| | | | ||||||  | ||||||||    || ||||||||||| ||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| |||| |                ||  ||   |  | |  |  | |||       ||| || |        |||||| |                         
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagagagaaaattttcctcgattcttttgatttcgtgctg----cttagaaatct-------ttgcgcag-------------------------

upper sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ37620 (Selaginella moellendorffii), 5'ss of exon 1
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttcccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg
         |||||  | |||||  | || ||||||||||| || ||||||||| | || |||||||| ||||| ||||| |||||||||   |||||||||| |   |    |    |     | |      |  ||    | |   |||||    | |                                        
---------ATGAATCTCTTCCGCTTAGCAGGGGACATGACGCATCTCCTCAGCATTGTGGTGCTGCTGCTCAAAATCCACACCATCAAGAATTGCGCAGgtatggtatggcatcgatcaaagaggc------gattcttctcaaaacttctaaacgcag----------------------------------------

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|211525033|gb|FL310988.1|FL310988
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211391276|gb|FL329715.1|FL329715
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211489227|gb|FL334521.1|FL334521
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211033083|gb|FL322682.1|FL322682
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|148995872|gb|EE035110.2|EE035110
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211015157|gb|FL318457.1|FL318457
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|32795152|gb|CD947388.1|CD947388
EST:     GATCCCTACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: GATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211276370|gb|FL349478.1|FL349478
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|32801793|gb|CD954029.1|CD954029
EST:     GATCCGTACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: GATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|71329461|gb|DR801451.1|DR801451
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|78117678|gb|DV536065.1|DV536065
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|32789380|gb|CD941616.1|CD941616
EST:     GATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: GATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|32804031|gb|CD956267.1|CD956267
EST:     GATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: GATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211286717|gb|FL323332.1|FL323332
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211293162|gb|FL323832.1|FL323832
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211301697|gb|FL323431.1|FL323431
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211304541|gb|FL359141.1|FL359141
EST:     CAGCGTAGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211211451|gb|FL362582.1|FL362582
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211009468|gb|FL312897.1|FL312897
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
EST: gi|211427803|gb|FL348319.1|FL348319
EST:     CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAG                         GCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT
genomic: CAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGT

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: 140

GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGTACCTGGACCTGTTTGTTCATTTTGTGTCTCTGTATAACACTGTCATGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGTACCTGGACCTGTTTGTTCATTTTGTGTCTCTGTATAACACTGTCATGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGTACCTGGACCTGTTTGTTCATTTTGTGTCTCTGTATAACACTGTCATGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgccctt ... tttcttgtagGCATATCTCTGAAGACACAGGAGCTGTATGCACTTGTTTTTGCAGCACGGTACCTGGACCTGTTTGTTCATTTTGTGTCTCTGTATAACACTGTCATGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttcccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcccc