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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaactaaacatcttgttttgatgggatctgctatgtca...

Basic information

species Zea mays
transcript GRMZM2G149952_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatcc----agctggatagttctactcttccctttcatctcagaataattg--ggttccatgtccttgaactaaacatcttgttttgatgggat-ctgctatgtca--------------------------------------
||||||||| ||||| |||||||||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||  |    ||      | |  |||| |    | |  |     |||   ||  ||| || |||  ||||   || ||| |  |||   |    | |||  | | |                                       
GATGGGTTACAAAAATCCTGTTCTTCTGCTTCATCCATTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtag

upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G28980.2 (Glycine max), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaactaaacatcttgttttgatggga---tctgctatgtca
|||||||||||| || ||||| ||  |||| |||||||||||||| | ||| ||||| |||||||| || |||  |||| ||||||| |||||||||||||| |         ||   | | |  |   | |  |||||   |  |   | |   |  | ||          |  ||||||||| | |   | |||| ||  |
GATGGGTTATAAGAATCCTGTCCTCTTGCTTCATCCACTGGGAGGCTACACCAAAGCTGATGATGTCCCACTTGATTGGCGAATGAAACAACATGAGAAGgtgtgtgatgtactaaaccaaatacttt-tatagtctcatggt--tgaagctatgtcactttctgtgcctttttctgttttgattgtaatctttgctttgcta

upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G38760.1 (Glycine max), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgg---gttccatgtccttgaac-taaacatcttgttt-tgatgggatctgctatgtca
|||||| ||||| || ||||| ||  |||| |||||||| ||||| | ||| ||||| |||||||| || |||  |||| |||||||||||||||||||||| |    |    |  ||    | |||  ||| ||   |     |||||   | | | | || | | ||  |  ||  |||||| |      |  ||||      
GATGGGCTATAAGAATCCTGTCCTCTTGCTTCATCCACTTGGAGGCTACACCAAAGCTGATGATGTCCCACTTGATTGGCGAATGAAGCAACATGAGAAGgtgtgtgtcaatttctttgcctttttctatttaattgtaatcgcattggtttgctacttttcttggcacacacgcacattgtttgtctccaaagatgctt-----

upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaa--ctaaacatcttgttttgatgggatctgctatgtca
||||||||| ||||||||| ||||| |||| |||||  | || || || ||||| || |||||||| ||| |   |||||| ||||||||||| |||||||||   |      |  ||  | | ||   | ||   | ||  | | || ||    | || |  ||  |||||  | || | |  |||  |            
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgta---aaaaaagttattg-attgttgtgtgtctcttgagtgtgagtgtgt---gtatcttgaaatgctaaatgtgtt-tatgaatgtaaaacag-------

upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggat--agttctactcttccctttcatct-cagaataattgggttccatgtccttgaactaaacatcttgttttgatgggatctgctatgtca
||||||||||||||||||| | ||| |||| |||||| ||||||| || |||||||| |||||||| ||||| || ||| ||||||| || || ||||||||||  | | | ||  |  |||  | || | | |  | | |    | |||       |||    |||| |     || ||  |||||  |             
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtatt-aacggaatcaaagtctttttttgcgtgttgtttgctagttcattataggagatgc---tgaattggttttcatgacttgattag-------------

upper sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaactaaacatcttgttttgatgggatctgctatgtca------------------------------
|||||| || || |||||||| ||  | || |||||| | ||||| |  ||||| ||||||||||| || ||| ||||||||||||||||||||||||||||         |||   | |  | |     |  || | | ||| | |    ||| | | |  |||     |||  |||  |      | || |  |   |                              
GATGGGCTACAAGAACCCTGTCCTCTTACTTCATCCATTAGGAGGCTATACAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAGgttcatgaactgatc-ctatgatgtattgctcaatttgaaaatcagtta--tccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcag

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|211414263|gb|FL322238.1|FL322238
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGARAAG                         GTTCTTGARGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCNATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32920504|gb|CF025316.1|CF025316
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32829670|gb|CD969348.1|CD969348
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32830909|gb|CD970587.1|CD970587
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32838969|gb|CD978650.1|CD978650
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTCCT-GAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32829388|gb|CD969066.1|CD969066
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32831832|gb|CD971510.1|CD971510
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|76287850|gb|DV027418.1|DV027418
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCACCCCAGAATCAACTGTTGTTCG-GATCTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTT-GCGATCTT
EST: gi|32829476|gb|CD969154.1|CD969154
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32829296|gb|CD968974.1|CD968974
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
EST: gi|32831003|gb|CD970681.1|CD970681
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTC

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: 46

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1423

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1161

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 73

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagct ... tttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggatagttctactcttccctttcatctcagaataattgggttccatgtccttgaactaaacatcttgttttgatgggatctgctatgtca

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagaataa