Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaccgtcgctcgctcctttgttccggatttcgcctgcctatctggcggcttcgccggttctaacgtgttgcttggtttgatggtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG

Basic information

species Zea mays
transcript GRMZM2G158918_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158918_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g34640.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------gtatgctaccg---tcgctcgctcc--tttgttccggatttcgcctgcctatctggcggcttcgccggttctaacgtgttgcttggtttgatggtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
                                         ||  ||| |||   | || |  | |  | | | || ||| ||||   | |  || |  ||| | | | ||    |  ||   ||| |||  |  | || | |||||||||||||||||||||||| || ||||| |
gtaatctctccccccgcccctctccctcccgcttccttactgttagcttccggatttgcgctgttcggtctctccctgatgtcgctgacgtgcctcgttgctgcccggcttggggctggtgtgttgttttctttttgtgtgtagATGTGGAGAAGTTCTACCAGCTCTGCGACCCAG
















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|211514713|gb|FL212182.1|FL212182
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|8368523|gb|BE051468.1|BE051468
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514724|gb|FL212193.1|FL212193
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211512367|gb|FL212177.1|FL212177
EST:     CCGCGACTTCCGCGNCCGCCGCGCGKNCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514719|gb|FL212188.1|FL212188
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGYCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514710|gb|FL212179.1|FL212179
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514723|gb|FL212192.1|FL212192
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211512366|gb|FL212176.1|FL212176
EST:     CCGCGACTTCCGC-GCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514718|gb|FL212187.1|FL212187
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514722|gb|FL212191.1|FL212191
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514711|gb|FL212180.1|FL212180
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|60342605|gb|DN209578.1|DN209578
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514716|gb|FL212185.1|FL212185
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514720|gb|FL212189.1|FL212189
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514717|gb|FL212186.1|FL212186
EST:     CGCGACTTCCGC-GCCGCCGCGCGGGCATTGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CGCGACTTCCGCGGCCGCCGCGCGGGCA-TGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211517069|gb|FL212195.1|FL212195
EST:     CGCGACTTCCGC-GCCGCCGCGCGKGCATNGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CGCGACTTCCGCGGCCGCCGCGCGGGCAT-GATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514712|gb|FL212181.1|FL212181
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211517068|gb|FL212194.1|FL212194
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|211514715|gb|FL212184.1|FL212184
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|60345474|gb|DN212447.1|DN212447
EST:     CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: CCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
EST: gi|21843468|gb|BQ704049.1|BQ704049
EST:     GCCGCGCGGGCATGATCAAGGCCCTCACCAACG                         ATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG
genomic: GCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG

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: 376

GACCCCGGCGCCGGCGCACACTACTCCGTCCGTACCGCGGAGGAGGTTTTCCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

GACCCCGGCGCCGGCGCACACTACTCCGTCCGTACCGCGGAGGAGGTTTTCCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GACCCCGGCGCCGGCGCACACTACTCCGTCCGTACCGCGGAGGAGGTTTTCCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 191

GACCCCGGCGCCGGCGCACACTACTCCGTCCGTACCGCGGAGGAGGTTTTCCGCGACTTCCGCGGCCGCCGCGCGGGCATGATCAAGGCCCTCACCAACGgtatgctacc ... gtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaccgtcgctcgctcctttgttccggatttcgcctgcctatctggcggcttcgccggttctaacgtgttgcttggtttgatggtttgcgcagATGTGGAGAAGTTCTACCAGCTGTGTGACCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG