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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattccaacctaagtagaaactgaatttgtcgtgtatctcttttttgttcacactgctgcatcacttgcttcctcattgatttctgttgaaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT

Basic information

species Zea mays
transcript GRMZM2G066496_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 7
tcattccaacctaagtagaaactgaatttgtcgtgtatctcttttttgttcacactgc-tgcatcacttg-cttcctcattgatttctgttgaa-atttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT
   |    | |  |   || |    || || | |   ||||| |||  | || |     | |||||   | ||||||||||||| |  ||| || || ||||||||||| |||||||||||||| ||||||||||| |||||||| || ||| | ||||||||| | |||   ||  |||||||||| ||||||||||| |||
---tcaatatcacatctgatataacatgtgccttacttctctgtttgctccatatgatgttcatcatccgtcttcctcattgatattagttaaacatgtgcagCATGCTGTACATAGAGACAGCTGATCGGCCTGGTCTACTTCTGGAAATAGTGAAGATCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGAT
















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|67011780|gb|CO440529.1|CO440529
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|67022635|gb|CO451384.1|CO451384
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32830465|gb|CD970143.1|CD970143
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32804124|gb|CD956360.1|CD956360
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|32859901|gb|CD999582.1|CD999582
EST:     ATCGATATTGCAACACATATAGTT-TTTAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|31558031|gb|CD527243.1|CD527243
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGNCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|148954707|gb|EC900159.2|EC900159
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAA
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGC-TTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAA
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|18164129|gb|BM333968.1|BM333968
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|89759755|gb|DY688471.1|DY688471
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
EST: gi|60359682|gb|DN226655.1|DN226655
EST:     ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG                         CATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT
genomic: ATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAAT

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: 183

GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 451

GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAGgtttggttct ... aaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcacactgctgcatcacttgcttcctcattgatttctgttgaaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT
                              cattgat  putative branch site (score: 255)
                                          ttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattccaacctaagtagaaactgaatttgtcgtgtatctcttttttgttcacactgctgcatcacttgcttcctcattgatttctgttgaaatttgcagCATGCTTTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
-cattcca
- - - - - - - - - -aactgaa
- - - - - - - - - - - - - - - - gtgtatc
- - - - - - - - - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg