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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattcaccagttccttttctctttggtaccgcctcaagtttttttttaaaaaaacatgtattaacctagaattatgcagctactatatttggatc...

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 7
TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattcaccagttccttttctctttggtaccgcctcaagtttttttttaaaaaaacatgtattaacctagaattatgca-gctactatatttggatc----
||||||||  ||||| |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||  | ||||||| ||||||||| ||||||| |||||| |    ||||||| |||||   ||     | ||||| ||||      |      ||    |   ||||| |  | | ||  || ||        
TGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGAACAATCATGGCCACAAGGATTGTCTCTTGCAGAGACCATGAAGTTTCAGTTCCCTCAGgtcagtattcatcttccccttttccctttg---cctatatatgttttcttttgggggtaagctctttg--ttgtgattatacttgtttctgaatgtgtcatgaat
















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|60349468|gb|DN216441.1|DN216441
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGC-ATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACCACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 242

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 194

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 149

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattcaccagttccttttctctttggtaccgcctcaagtttttttttaaaaaaacatgtattaacctagaattatgcagctactatatttggatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA