Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttccctgcctcttgacccttgtgccttgttttctcgttctgaaaatagggtcacgttagctaagcttccatgatttgttgaattgggcggaatt...

Basic information

species Zea mays
transcript GRMZM2G031824_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 1
CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttccctgcct----cttgacccttgtgccttgttttctcgttctgaaaatagggtcacgttagctaagcttccatgatttgttgaattgggcggaatt
 ||||  ||||| |||||| |   ||||||||||||  |||||||||| ||||| || ||||||||||||||  |  |||| ||||| || || |||||||||     |||  |       | ||  | |||  |  |        | |     ||   ||    |||| |    |     | || |  |  | |     ||||
GTGGAGCGGCGCCTGCTTCGCCCGGAACGAGGCCGCGCTCGAGCTCACCCCCGGAGATCGCAACGGGACCGAGCTGAGCGGCGCCGTGCTCCGACTCAAGgttttgcccccaactcaggattggaatcgtgtcgcggggggcggtttccgccggatgtcgtggaattaggtggaatc----ggttgggcgtgtggttgtaaatt
















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|149104788|gb|EE290251.2|EE290251
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|71775022|gb|DR972900.1|DR972900
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|149007773|gb|EE040269.2|EE040269
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCCACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|78111913|gb|DV530309.1|DV530309
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|71430819|gb|DR811869.1|DR811869
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|32839581|gb|CD979262.1|CD979262
EST:     TACT-CGCCTCAAG                         ACTGCTTCA-CTCATAGTTGGGCGTGCATGGATCTCTACGTTNTTTGCAAC
genomic: TACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTT-TTTGCAAC
EST: gi|148973114|gb|EE024181.2|EE024181
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|149100419|gb|EE186494.2|EE186494
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|211056023|gb|FL008159.1|FL008159
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCGTGCATGGATCTCTACGTTTTTCGCAAC
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTT-GCAAC
EST: gi|148940292|gb|EC885074.2|EC885074
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|71429323|gb|DR810373.1|DR810373
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|78076415|gb|DV504849.1|DV504849
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|149078582|gb|EE167366.2|EE167366
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|211056025|gb|FL008161.1|FL008161
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCGTGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|32842171|gb|CD981852.1|CD981852
EST:     GTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCGTGCATGGATCTCTACGTTTTTGCAACA
genomic: GTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|211056020|gb|FL008156.1|FL008156
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCA-CA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|78075988|gb|DV504422.1|DV504422
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|148996938|gb|EE035750.2|EE035750
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|78121398|gb|DV539782.1|DV539782
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCGTGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|211116070|gb|FL397775.1|FL397775
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTC
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTC
EST: gi|211063418|gb|FL406485.1|FL406485
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTC
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTC
EST: gi|211056027|gb|FL008163.1|FL008163
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|32840051|gb|CD979732.1|CD979732
EST:     ACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGCTGGGCGTGCATGGATCTCTACGTTTTTGCAACA
genomic: ACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
EST: gi|78113167|gb|DV531561.1|DV531561
EST:     CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAG                         ACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA
genomic: CCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACA

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), 46 (downstream exon)
Score: 135

CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttcc ... gtttatgcagACTGCTTCAGCTCATAGTTGGGCATGCATGGATCTCTACGTTTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAAAGGCGCGTGCTTCTCGGAGAACGAGGCCGCTATCGAGCTCACGCCCGGGGACCGCAACGGGACCGACGTCGGCGGTGCCGTACTGCGCCTCAAGgttcccttccctgcctcttgacccttgtgccttgttttctcgttctgaaaatagggtcacgttagctaagcttccatgatttgttgaattgggcggaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatag