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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcctgcctacatcatcacaaagaactttctgcctcataagatcttcgttcgtgtaaatttgtttaaaccagggcttcctttccatgcag

Basic information

species Zea mays
transcript GRMZM2G101502_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101502_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g43100.1 (Oryza sativa), 5'ss of exon 6
TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcctgc---ctacatc---atcacaaagaactttctgcctcataagatcttcgttcgtgtaaatttgtttaaaccagggc-ttcctttccatgcag
| ||||||||||||||||||| |||||||| |||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| |||||  |||||||||||| | | | |   | |   |   |||| | ||||     |   | |  || | |  |    |||  |     ||   |   |   |||| ||||||||||
TCTGGAGGAGTTTGCAAAGGACCCTGAGCCAATAGTCTCCCAGAGCTGCGAAGTAGCACTCAGCATGCTTGAATATGAGAGATCAGGGAAGGCCTTTGAGgtacatacatacacgccaggcctagatcaaacagaaaagcatttgtaactagctttgtggcattgtctaacacattgtgctgtgttgttccattccatgcag

upper sequence: GRMZM2G101502_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g06620.1 (Oryza sativa), 5'ss of exon 7
TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcctgcctacatcatcacaaagaac-tttctgcctc-ataagatcttc--gttcgtgtaaatttgtttaaaccagggcttcctttccatgcag
| ||||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| |||||||| || |||||||| || |||||||| ||||||  | ||   ||| |||| || ||| ||| ||| |||||   |   ||| ||      |  |   ||||||  |  |||                  
TCTGGAGGAATTCGCGAAGGATCCTGAGCCTATAGTCTCCCAAAGCTGTGAAGTCGCGCTCAGCATGCTCGAATACGAGAGATCCGGAAAATCCTTCGAGgtatattcc---ctagatcaacagaaataacctttgtgcctttgtggtatcgtctaaccggcttgtgtttgttccatgcag------------------

upper sequence: GRMZM2G101502_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0005g03050.t01 (Vitis vinifera), 5'ss of exon 6
TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct----gcctacatcatcacaaagaactttctgcctcataagatcttcgttcgtgtaaatttgtttaaaccagggcttcctttccatgcag
| | |||||||| || |||||||||||||| || ||||| |||||||||||||| |||||||  ||||| || | ||| ||||| || ||||||||||||||| |    |      ||   | |  || ||  |   |  |   | |    |     |||  |  || |   |   | ||     | | ||||||||||
TCTTGAGGAGTTCGCCAAGGATCCTGAGCCTATCGTCTCACAGAGCTGTGAAGTTGCTCTCACCATGCTGGAATTTGAAAGATCTGGCAAATCCTTTGAGgtatgcaaatcagaaactgacttaaaaccaatcatcataagaaactttgatttgattttcaggagaaatgactctcatcaaa---tgcattccatgcag

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|78106815|gb|DV525233.1|DV525233
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|71436021|gb|DR817071.1|DR817071
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|94472329|gb|EB701287.1|EB701287
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|76914576|gb|DV165581.1|DV165581
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|78078332|gb|DV506747.1|DV506747
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTTTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|74246445|gb|DT654359.1|DT654359
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|74236077|gb|DT643991.1|DT643991
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTTTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|60398795|gb|DN231611.1|DN231611
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|32797957|gb|CD950193.1|CD950193
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|76293314|gb|DV032882.1|DV032882
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTTTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTTTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
EST: gi|211453881|gb|FL033204.1|FL033204
EST:     AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAG                         TTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA
genomic: AAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGA

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: 46 (upstream exon), 46 (downstream exon)
Score: 35

TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGATGATCACTCAATGCGAAGTGACTGAAAGCTTCTTGTATTGGTTAATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGATGATCACTCAATGCGAAGTGACTGAAAGCTTCTTGTATTGGTTAATGTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 73

TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGATGATCACTCAATGCGAAGTGACTGAAAGCTTCTTGTATTGGTTAATGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcct ... ttccatgcagTTTCTCTTCCTTCAGACTCCTCATGTGCAGTCCTAGGTTCCTCTTCGTCGATGATCACTCAATGCGAAGTGACTGAAAGCTTCTTGTATTGGTTAATGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGAGGAGTTTGCAAAGGATCCTGAGCCCATAGTCTCGCAGAGCTGTGAAGTAGCTCTCAGTATGCTCGAGTATGAGAGATCGGGGAAATCCTTTGAGgtacgtgcctgcctacatcatcacaaagaactttctgcctcataagatcttcgttcgtgtaaatttgtttaaaccagggcttcctttccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC