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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaaagttggatgtcttttcaggactcgtacatgtttgctaacctaacatgcaatattttgtatgcag

Basic information

species Zea mays
transcript GRMZM2G111477_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtgg---caagaaagttggatgtcttttcaggactcgtacatgtttgctaacctaacatg-caatattttgtat-gcag
 |||||||| ||||| |||||||| |||||||| |||||||||| ||| || ||||| ||||| ||||||||||| ||||||||||||||||||||||||||  ||  |    || ||  |   || || | |   |     | | | | ||  | |  ||| ||   | |  || | | ||||
AGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTTGAAGgtttgggagggataataacttctcatttcctgttttgctgatttcttctctgggagcaaaacctgatgacaacttattttgcag

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccg-gtggcaagaaagttggatgtcttttcaggactcgtacatgtttgctaacctaacatg-caatattttgtatgcag--------------------------------------------------------------------------------------------------------------------
||||||||||||||| ||||||||||  ||| | |||||  | || || || ||||| ||||| ||||| ||||| || ||||| || ||||||||||||||  | ||         | ||  | || ||| ||  ||   | |   ||| |   ||   | | || || |    |   ||                                                                                                                    
TGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagatcttccatagcattgtt--tctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcag

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaaagtt-----ggatgtcttttcaggactcgtacat-gtttgctaacctaacatgcaatattttgtatgcag---------------
||||||||||||||| ||||| || || ||| | |||||| | || || || ||||| ||||||||||||||||| || || || || |||||||| |||||  | |  |    || ||     |  |  || || ||  |   || || |  |  | |    |      || || || | | |                
TGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgttagttttctctgaattttttctgatttcctctttagctcctctaaatcgcattttgattacattacggatcttgtggaaggaaaaccagcaccagatt

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaaagtt-----ggatgtcttttcaggactcgtacat---gtttgctaacctaacatgcaatattttgtatgcag-------------
||||||||||||||| ||||||||||  ||| | |||||| | || || || ||||||| ||| ||||||||||| || || || || |||||||| |||||| | |  |    || ||     |  |  || || ||  |    | ||    |||  ||  || |||     ||| ||||     |             
TGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgtcagttttctctgaattttttctgatttcctctttagctcctccatattgcattttttatgcttacactttgtatcttgtggaaggaaaaccagcacca

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 14
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaaagttggatgtcttttcaggactcgtacatgtttgctaacctaacatgcaatattttgt----atgcag
||||||||||||| | ||||| ||||| || ||||| ||  |    ||||| ||||| |||||||| |||||||| ||||||||||| || ||  | |||||         |  |  |||    || |  |  | |    |||  ||    || || |||  ||| || ||      ||||||
TGGTGTTGCTCTTTTGTATGCTTCGAAAGAACTTGAGAAGCTTTCCACAGCTAACTTTGATCAGAAAATTGGTGTTCAAATCATTCAAAACGCACTCAAGgtgtttctctcatcacattgttcatcctcgctag-cataaacagcttctagaatcttacacacaaaatctttctttgatgcag

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtg---gcaagaaagttggatgtcttttcaggactcgtacatgtttg---ctaacctaacatgcaatattttgtatgcag----------------------------------------------------------------------
||||||||||||  | ||||| ||   ||||||||||||  | || || |||||||| ||||||||| |||| ||||||||||| |||||||| |||||||| |  |    ||||     |  |  ||   ||    |   | ||   | ||   |  || ||  |     |||| | |     |                                                                      
TGGTGTTGCTCTATTGTATGCTTCCCGGGAGCTTGATAAGATTCAAACCGCGAACTTTGATCAGAAGGTTGGAGTGCAAATCATCCAGAATGCCTTGAAGgtactttttgtgcaacttgatctggagtgagtttgtaaaatgaacgaatctgtatcggacttaggagaggctattgtcttgatcgcatcagcttatgtgtcctctttactgggagtaaaatttcggtgaaatgtaatgagcatgttgtactgcag

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc--aagaaagttggatgtcttttcag-gactcgta--catgtttgctaacctaacatgcaatattttgt-atgcag-----------------------------------------------------------------------------------------------------------------
|||||| |||||| | ||||| ||    ||||| || ||| | || || |||||||| || |||||||| || ||||||||||| || |||||||||| |||    |  |  ||   |   | |    |   ||  |||| ||   ||| |  | ||  ||   | | | || ||  | | |  |                                                                                                                 
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttctcaacctacccgtagaagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag

upper sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S378_9V6.1 (Physcomitrella patens), 5'ss of exon 14
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaa---agttggatgtcttttcaggactcgtacatgtttgctaa-cctaac-atgcaatat--tttgtatgcag--------------
||||||||||||| | ||||| ||   ||||||||| ||  | || ||  | |||||||| |||||| |||| |||||||| ||||||||||| || |||||    |    |        |||   |    || |    | |||   ||   || |  |||   ||||| ||   | |||  | ||              
TGGTGTTGCTCTTTTGTATGCTTCACGGGAGCTTGACAATGTTCAAACTTCAAACTTCGACCAGAAGGTTGGAGTGCAAATTATTCAGAATGCCTTAAAGgtattattttgatttcctgtttgagggcgccttaatagtttgtagtagtgctctgagtctagttatgcattacgatctgtgagaaggtagtgtaatttgc

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|76020164|gb|DT947334.1|DT947334
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|74236027|gb|DT643941.1|DT643941
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|76020163|gb|DT947333.1|DT947333
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|113703063|gb|EE680567.1|EE680567
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|67018599|gb|CO447348.1|CO447348
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|74236026|gb|DT643940.1|DT643940
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|15057239|gb|BI361211.1|BI361211
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|5108264|gb|AI739977.1|AI739977
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|60394542|gb|DN227412.1|DN227412
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|37400119|gb|CF637406.1|CF637406
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|211121936|gb|FL439136.1|FL439136
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTGTACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|78119934|gb|DV538318.1|DV538318
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|60348034|gb|DN215007.1|DN215007
EST:     CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT

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), 47 (downstream exon)
Score: 390

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTAGGAAAGCTTTTGGAGCAAGAAAATACTGACCTGGGTTATGATGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 204

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTAGGAAAGCTTTTGGAGCAAGAAAATACTGACCTGGGTTATGATGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTAGGAAAGCTTTTGGAGCAAGAAAATACTGACCTGGGTTATGATGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 208

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc ... ttgtatgcagACACCTGTACACACAATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTAGGAAAGCTTTTGGAGCAAGAAAATACTGACCTGGGTTATGATGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggcaagaaagttggatgtcttttcaggactcgtacatgtttgctaacctaacatgcaatattttgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG