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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaagacagccaccctttgtctcgcctccgtttctcctcctgggctcctggcacgagatctcctccctagcgctttgtgtgtttggggatcgcg...

Basic information

species Zea mays
transcript GRMZM2G146951_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146951_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 1
---------GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaagacagccaccctttgtctcgcctccgtttctcctcctgggctcctggcacgagatctcctccctagcgctttgtgtgtttggggatcgcg---
         ||||  |||| ||||| |||| || ||||||         ||||||  || |||| | |||||||||||||| ||||||||||||||  ||||||| |||||  ||  |   |  |  ||  |  |||| |||   |      ||  ||  |  |  | |     |   |   |     ||   |  | ||||| | | |   
GGCGGCGATGGCGCTGGCCATCGCCCTCGCGGCGCTCTGC---------CTCGCGGGGCTGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgccca---ctccttcctctactctcccctttatcctctttcacggcatgatctctccgctgcgtttgttttttttttgtcggatctggggttggggtgg
















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|78115833|gb|DV534221.1|DV534221
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|149012081|gb|EE042501.2|EE042501
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|22491002|gb|BU050925.1|BU050925
EST:     CTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|31353915|gb|CD438272.1|CD438272
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|149095226|gb|EE180848.2|EE180848
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|148999936|gb|EE036993.2|EE036993
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|148971253|gb|EE022114.2|EE022114
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|149080734|gb|EE169796.2|EE169796
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|13237044|gb|BG355058.1|BG355058
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|13237179|gb|BG355193.1|BG355193
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|91871350|gb|EB401373.1|EB401373
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|19437149|gb|BM953559.1|BM953559
EST:     CTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|148959757|gb|EC905651.2|EC905651
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
EST: gi|149023680|gb|EE045933.2|EE045933
EST:     CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAG                         AAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA
genomic: CGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAA

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: 318

GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAACTTCCCTACTCCTACTATTCTCTCCCATTCTGCAAGCCGGATACCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAACTTCCCTACTCCTACTATTCTCTCCCATTCTGCAAGCCGGATACCATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 328

GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAACTTCCCTACTCCTACTATTCTCTCCCATTCTGCAAGCCGGATACCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1197

GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaa ... atcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAACTTCCCTACTCCTACTATTCTCTCCCATTCTGCAAGCCGGATACCATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaagacagccaccctttgtctcgcctccgtttctcctcctgggctcctggcacgagatctcctccctagcgctttgtgtgtttggggatcgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcctcc
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctccc