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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccgctctgctagtctctgactctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG

Basic information

species Zea mays
transcript GRMZM2G177912_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 9
gtaatccgctctgctagtctctgactctttgttgtgatactta-actct-atcttgtgtgtcttgttgtctgatctctctattg-catcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG
||||||   ||| ||  |   |      |  | || | | ||  ||| | ||      | |  | |  | || | | | | ||  ||||||||||| ||||| || || |||  |||||| || |||||||| ||||||||| | ||||| || || ||||||||||||||
gtaatctattctactgttacgtagtatatgatagtcaaatttgtactttgatgcctgatctaatatcatatgctgtttatgttttcatcagTCTGCTGTTCTAGCACCTTCTCAAAAGGGTGAAAAGAAAGTAAGGAGCATCCTGGAGGAACTCTGTGGCAATGTCCATAG
















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|148969237|gb|EE019991.2|EE019991
EST:     GCATATTTGTAGAGAGCATTTTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATT
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|211233368|gb|FL465080.1|FL465080
EST:     AGAGGGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTAAGGAGCATC
genomic: AGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|60338311|gb|DN205284.1|DN205284
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|37397643|gb|CF636126.1|CF636126
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|211430021|gb|FL445207.1|FL445207
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTAAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: GCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
EST: gi|78120130|gb|DV538514.1|DV538514
EST:     CATATTTGTAGAGAGCATTCTTAGAT-CGGGTCTGCCGCCATGGTTCCTG                         TCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC
genomic: CATATTTGTAGAGAGCATTCTTAGATAC-GGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATC

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: 126

GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 153

GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTGgtaatccgct ... attgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG
                                      tctctctatt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatccgctctgctagtctctgactctttgttgtgatacttaactctatcttgtgtgtcttgttgtctgatctctctattgcatcagTCTGCCGTTCTTGCTCCGTCTACAAAGGGCGAGAAGAAAGTGAGGAGCATCTTAGAGGACCTTTGCGGCAATGTCCATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA