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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttcccttaataaatatgacacaatatggatctgcatatagcatcagcatgctttcacttctttaaagttcatgagttcaatagttttaatctg...

Basic information

species Zea mays
transcript GRMZM2G558539_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G558539_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 6
GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttcccttaataaatatgacacaatatggatctgcatatagcatcagcatgctttcacttctttaaagttcatgagttcaatagttttaatctg------------
|||||||||||||||||||| ||||| ||||||| |||||| ||||||||||||||||| ||||| || ||||||||||||||||||||||||| || ||| |     || ||      ||||  |||    | | |||| | ||||  |||| ||     | |  |||| ||| |||| ||   |  ||            
GCTGCTAAAAGGCATTTGACTCAGCGTATTGAAAGGTTGGATGATAAATTGGATCAGCAAAAGGCGCTTTCTGGACAAATAAGAGATGATgtactttctcctt-----aacat----tcatatcaatccatgtttggcattaacatgtcttcattttc---acgcgcatgggttgaataattaagaaatgtctagtagcata

upper sequence: GRMZM2G558539_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0026g01700.t01 (Vitis vinifera), 5'ss of exon 7
GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttcccttaataaatatgacacaatatggatctgcatatagcatcagcatgctttcacttctttaaagttcatgagttcaatagttttaatctg---
||  | |||||||||||||||||||| ||||| || ||||| |  ||| ||||| |||||||||   | ||      ||| |   |||| |||| |   ||   |||  |  |  |  | | |       | ||  |  |  | ||  | |  ||     | |    |      ||| |  |  | | |    
GCAACAAAAAGGCATTTGACACAGCGAATTGAGAATTTGGATGGAAAACTGGATGAGCAGAAGGAGATCTCGAAGTTAATTAAGAATGAGgtacat---ccaaaaatctacctcccttattgtattatgccctaatgagtttgtatcttatatctaagaaacaacgtaaagcaacaaaaaataaagttttttt
















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|60339589|gb|DN206562.1|DN206562
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|60358480|gb|DN225453.1|DN225453
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|86471474|gb|DY237844.1|DY237844
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|5936814|gb|AW060082.1|AW060082
EST:     GATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: GATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|76925222|gb|DV170325.1|DV170325
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|32827822|gb|CD967500.1|CD967500
EST:     ACGATAAATTGGATCAGCAAAAGGCTCTATCTGGACAAATAAGAAATGAT                         GTTACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAAT
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAAT
EST: gi|71300395|gb|DR786266.1|DR786266
EST:     GATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: GATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|60340147|gb|DN207120.1|DN207120
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|86474502|gb|DY240872.1|DY240872
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|110944775|gb|EE164932.1|EE164932
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|32929416|gb|CF034228.1|CF034228
EST:     ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCATTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
EST: gi|71332095|gb|DR802954.1|DR802954
EST:     ATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGAT                         GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC
genomic: ATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAAC

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: 169

GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttc ... acctattcagGTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTAAAAGGCATTTGACACAGCGCATTGAAAAGTTGGACGATAAATTGGATCAGCAGAAGGCTCTATCTGGACAAATAAGAGATGATgtaccttttcccttaataaatatgacacaatatggatctgcatatagcatcagcatgctttcacttctttaaagttcatgagttcaatagttttaatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG