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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgggacgccgcaacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG

Basic information

species Zea mays
transcript GRMZM2G058948_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 9
ccatgggacgccgcaacgcct--caaaaaccatgcccagttt--acacctccttttgatctgtttgatcc--ttgagacctttgtgcaatacgtgt-ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
           ||||  | ||  | | |||||||    ||    |      ||||| |||| |||  | |  || | || ||  | ||  |  | |  || |||||||||||||||||||||||||||||||| |||||||||||||| || |||||| ||||||||||||| |||||||| |||||||||||||||
-------ttctcgcagagtctttccataaccatgtggtgtcgcaatgttctctttttatctttttctttctgtttaaactttcttacacaatttctgcttcttatagGTTGGTTTCCAAGCAATAGCAGAAGCTATGGGAATGGCTGCTGTAAAAGCAATAGCTGCTATAACAGCCATAATCGCTGGAGGTCGTCTG

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 9
ccatgggacgccgc-aacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
|     ||    ||        || | |           | |        |  ||  | |  |       | |    |  |       || | ||||  || |||| || ||||| || || |||||  | ||  | |||||||||||||||| ||  ||||| ||||| ||||||||||| || ||||| 
ctggttgaaattgctggtatgccagatatttctatatactcaaggaagtctaggaaatatcagtggtcgcaaaatgctaagtttctactgctctttt-cagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGGCTTGCTGCAGTCAAAGCAGCAGTGGCTATTACTGCAATAATTGCTGGTGGCCGTCTA

upper sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 8
-ccatgggacgccgcaacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
  |||| |  ||    |            |||      |  |     ||| |  ||   ||||      ||||    |  |           ||||   || |||| || ||||| || || |||||  | ||| | |||||| ||||||||| || |||||| |||| |||||||||||| || ||||| 
ctcatgtgttgctaatatttgctgtcttgcatatttc-tcaaggaagcctataaattattttgtaagaggagaatgctaagttgctaactacttttctcagATTGGATTTCAAGCCATTGCTGAAGCTCTTGGACTAGCTGCAATCAAAGCAGCAGTTGCTATCACTGGCATAATTGCTGGTGGCCGTCTC

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|71449648|gb|DR830698.1|DR830698
EST:     TCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGG                         GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCA
genomic: TCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCA
EST: gi|74240304|gb|DT648218.1|DT648218
EST:     TCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGG                         GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCA
genomic: TCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCA

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: 176

GATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGGgtaaccattt ... ttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG
                                          tgttttttt  CT-rich tract
                                          tgtttttttata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgggacgccgcaacgcctcaaaaaccatgcccagtttacacctccttttgatctgtttgatccttgagacctttgtgcaatacgtgtttttttatagGTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
ccatggg
- - - - cgccgca
- - - - - - - - - - - - - - catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatcct