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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctttggatgtctgttggctacacttcttggtttacatttgtattctgttgtttgtgtatttctcatttcttcgttaacacttaacaaacatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 2
tgcctttggatgtctgttggctacacttcttggtttacatttgtattctgttgtttgtgtattt---ctcatttcttcgttaacacttaacaaacatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG
    ||   ||  ||||||   | |||||||| |  | || |||| |||| || | |  | |     ||| ||| ||  || |||||||| ||||||||||||||||||||||| ||  ||||||||||||||||||| ||| ||||||| || || || |||||||| || ||||| |||||||||||| |  ||||||| |
--atttgatatcactgttgatga-acttcttgatgcatatatgtaatctgctgctcgcatctcctgcctctttttttttttgacacttaataaacatgtgcagATGGTGTGCTCAACAGGCCTTCTTTATGTTCTGAGGCGGCTAAAGATAATTTCATTTACAAATAGCGAGCCATCCGTGCCTTCTGATGCGTTATTCTTCG
















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|71298002|gb|DR784970.1|DR784970
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|31353270|gb|CD437627.1|CD437627
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|78115509|gb|DV533897.1|DV533897
EST:     TCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCCACGCTCCTTCCG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: TCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATC-ACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|71767957|gb|DR965894.1|DR965894
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|71420101|gb|DR805011.1|DR805011
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|93282589|gb|EB674853.1|EB674853
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|78076866|gb|DV505300.1|DV505300
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|31355902|gb|CD440259.1|CD440259
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|148947455|gb|EC892886.2|EC892886
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         ATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
EST: gi|74233567|gb|DT641481.1|DT641481
EST:     CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAG                         AGGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC
genomic: CTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATC

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: 48 (upstream exon), 48 (downstream exon)
Score: 87

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 152

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 184

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 158

TGCTGCTAGTGATGTTTAACAAAGCAGCTCTTTCTTCATACAAATTCCCTTGCGCAAATGTCATCACGCTCCTTCAGgtactggatg ... acatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttgtttgtgtatttctcatttcttcgttaacacttaacaaacatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG
                                    acttaac  putative branch site (score: 158)
                                      ttaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctttggatgtctgttggctacacttcttggtttacatttgtattctgttgtttgtgtatttctcatttcttcgttaacacttaacaaacatgtgcagATGGTGTGCTCCACGTGCCTTCTTTATGTTCTGAGACGGTTAAAGATCATCTCCTTCACAAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTG

tgccttt
- - - - - - tctgttg
- - - - - - - - - -gctacac
- - - - - - - - - - - - - - - - - -tacattt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt