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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcctagttttttatgcattcaagatcataaaagtgctaactgtttctttgctgttttaacag

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 9
ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc----tagttttttatgcattcaagatcataaaagtgctaactgtttctttgctgttttaacag---------------------------
||||||||||| ||||||||||||||||||||||||||||| || ||||||||||||||||||||||||| ||| |||    |  |||||  ||  | ||   |     |  ||  |  |    | |     | | |||                             
ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCTTTTCCTTTCAAAGGAAAATCTTTGGCgtgagtctcccctattctttttcttgtgtgcattctgcctgagatgtcatgtaggccgtaaagttgtaaacgacactagatgtgaggaactacaaaattt
















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|149076952|gb|EE165608.2|EE165608
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAA-TCTTTGGC                         TGGGATTTTACCAGCAATTGATGT
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGT
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|149104176|gb|EE289610.2|EE289610
EST:     CAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: CAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|71322126|gb|DR797758.1|DR797758
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|37400724|gb|CF637721.1|CF637721
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|113702575|gb|EE680079.1|EE680079
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAGGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCATGAATGCTATTGTTGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|78112245|gb|DV530639.1|DV530639
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|78180134|gb|DV550507.1|DV550507
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|76927276|gb|DV171212.1|DV171212
EST:     GTGTGGGCAGCGGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|5847119|gb|AW000198.1|AW000198
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|60396504|gb|DN229373.1|DN229373
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCNAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|32851209|gb|CD990890.1|CD990890
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|37374257|gb|CF623473.1|CF623473
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|78081464|gb|DV509876.1|DV509876
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|76289052|gb|DV028620.1|DV028620
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|5343187|gb|AI795372.1|AI795372
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|91876330|gb|EB406287.1|EB406287
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
EST: gi|8551590|gb|BE128935.1|BE128935
EST:     GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC                         TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG
genomic: GTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 910

ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 618

ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 511

ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 1072

ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcc ... gttttaacagTGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGCgtaagtatcctagttttttatgcattcaagatcataaaagtgctaactgtttctttgctgttttaacag

- - - - - - - - - - - - GCAGCT
- - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA