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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcagttccatgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 12
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcagttccatgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag
| ||||||||||| ||||||||||||||||| || ||||| |||||||| ||||||||| | ||||||||||||||||| ||||||||| |||| ||||||| |  | |  | | |||     ||||  |  ||    || || || || || ||||| |||   ||| |    | | |  |||
CCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCAAACCCAATAGGAGGAAGgtgatgtgatctacttgctcaggatgt--tttcaaacaattgttttgagcaatatacttaattttatcat----gttattgcag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G03920.1 (Glycine max), 5'ss of exon 11
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttca--------gttccatgcat--gccatgtag-taccagtgcatggtgttaagaaagatact------gaatgcaatcgtccttgatctcacag-----------------------------------------------------------------------------------------
| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||  | |||  |||||||||||| ||||| || || || |||||||||    |        ||| |||| ||  |  || | | | | |||      |||| |  |   | |       || | |||  ||| |  |  |   |                                                                                          
CCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCAAATCCTGTTGGAGGAAGgtaagcaaatatgcaaggttgcatgtatctggaatctggctgcaagttggcattgttcatcagtgtcccagctaagatttcaactgtcatacacattgaaagatattaccatgagtattgatatatggttttgatccttttttcaagcatttaagctttactcttaaattaacttttctttgacttgcag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 11
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcagttcca----tgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag--------------------------------------------------------------------------------------------------------
| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||  | ||   |||||||||||||||||| || || || |||||||||    |  |  |    ||||||        | | |||      |||| |  |   | |    |   ||  ||     ||  |||                                                                                                         
CCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCAAATCCTGTTGGTGGAAGgtaagcaaatatgtaaggttgcatgtatctggctgcaagttggcactgtttatcagtgtcccagctaagatt-tcaacagtcatacacattgaaagatattggatgtactatgagtattgatttatggttttgatccatttttctagcatctaagctttactcttaaatttaactttttcttggacttgcag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaa-cttcagttccatgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag
| ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||| | |||  |||||||||||| || || ||||| || ||||||||| ||  |     ||||    |||  |     | |   |  | || |    | || |   ||     | | |||      |||
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattttgatcttgctaatt--tgtttgtgacattgcaacttcag

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|211172446|gb|FL130947.1|FL130947
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211351173|gb|FL066633.1|FL066633
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCNAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTC
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTC
EST: gi|211174125|gb|FL130962.1|FL130962
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|32932509|gb|CF037321.1|CF037321
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211172448|gb|FL130949.1|FL130949
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|33093214|gb|CF053208.1|CF053208
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211174123|gb|FL130960.1|FL130960
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATC
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATC
EST: gi|211174124|gb|FL130961.1|FL130961
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211172450|gb|FL130951.1|FL130951
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|32943927|gb|CF048746.1|CF048746
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211174121|gb|FL130958.1|FL130958
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211174118|gb|FL130955.1|FL130955
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|30306555|gb|CD001228.1|CD001228
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211174117|gb|FL130954.1|FL130954
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|29544563|gb|CB604943.1|CB604943
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211174122|gb|FL130959.1|FL130959
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACAT--ACTCAGAATGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211172447|gb|FL130948.1|FL130948
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|18450515|gb|BM428793.1|BM428793
EST:     GTTA-TGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAA-TGACGGATCCCAT
genomic: GTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|29544433|gb|CB604813.1|CB604813
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACG
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACG
EST: gi|211174120|gb|FL130957.1|FL130957
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT
EST: gi|211172449|gb|FL130950.1|FL130950
EST:     CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAG                         GTATGATTCATCAAAGACATTCACTCAGAACGTCGAATTGACGGATCCCAT
genomic: CTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCAT

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: 297

CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 22

CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 26

CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcag ... gatctcacagGTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaacttcagttccatgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC