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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagaccccgtcccctgaccctgcccttcgcattgtggactcgggggcggaattgtctgggagccgcggagagcgcgatgtttcctgaggaataccttt...

Basic information

species Zea mays
transcript GRMZM2G061419_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061419_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 5'ss of exon 1
GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagaccccgtcccctgaccctgcccttcgcattgtggactcgggggcggaattgtctgggagccgcggagagcgcgatgtttcctg-----aggaataccttt---
||||| | ||||| |||| ||||| ||||||| ||||||  ||||||||||||||||||| ||||||    || ||   ||| ||  ||||||||||||||||||    || ||||   |  |||  |  | |||||   | |||| || |        ||  | ||| || |   |||  | | |||     |    | |||||   
GCCGCCGGCAATGGCGGCAATGGAGGCCGCCGCCGACGCGGTGCTCGCCGCCGCGAGCCGCGCCTTCTGCGGCCCCGCCGCCGTCTTCATCCAGATCCAGgtgagcgagcgcccccccgcattgcg-tcggaattgtt--cccgggagcagcgg-----ggagggcgccgaaatttcgaactgttctgttactatcggtgcctttttt
















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|71427423|gb|DR808473.1|DR808473
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|149109830|gb|EE293624.2|EE293624
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|149075471|gb|EE163995.2|EE163995
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|76913089|gb|DV165003.1|DV165003
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|74245609|gb|DT653523.1|DT653523
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|78090711|gb|DV519085.1|DV519085
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|148972415|gb|EE023349.2|EE023349
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|89251455|gb|DY623241.1|DY623241
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|71304141|gb|DR788190.1|DR788190
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|71447226|gb|DR828276.1|DR828276
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|71427209|gb|DR808259.1|DR808259
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|211431296|gb|FL159140.1|FL159140
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|76020824|gb|DT947994.1|DT947994
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|149076827|gb|EE165480.2|EE165480
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|148965663|gb|EE016513.2|EE016513
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|148969660|gb|EE020524.2|EE020524
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATACAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
EST: gi|76293199|gb|DV032767.1|DV032767
EST:     CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAG                         GGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT
genomic: CCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATT

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: 45 (upstream exon), 49 (downstream exon)
Score: 195

GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATTGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATTGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATTGTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 138

GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagacccc ... atttatgtagGGGTGCATGATCTGTTTAGTCCTTGCTCTCGGGTGGGCGGCTGCTTCAATTGTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCGGACAATGACGGCGATGGAAGCCGCCGTCGACGCTATGCTCGCCGCCGCGAGCCGTGCCTTCACGAGCACCTTTGCCATCGCCATCCAGATCCAGgtgagaccccgtcccctgaccctgcccttcgcattgtggactcgggggcggaattgtctgggagccgcggagagcgcgatgtttcctgaggaataccttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctgcc