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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaatcatttgaagcttgttggtccttaacccttgttatctgggtaatgatagtcatattgatatctgtgaatttatttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA

Basic information

species Zea mays
transcript GRMZM2G451366_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 7
gtatgttaatcatttgaagcttgttggtccttaacccttgttatctgggtaatgatagtcatattgatatctgtgaatttatttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA
||||||| | ||||| |||| ||||||| | ||||  || |||  ||   || |  |||||  || | | || ||||||  ||||||||||||| || || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| 
gtatgttgaccatttcaagcatgttggtgcataacagttattagttgt-caagggcagtcacttttacacctctgaattcttttgctttcagGATTTCTCTGATGTCTCTAAAGAGATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGG
















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|32847269|gb|CD986950.1|CD986950
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841613|gb|CD981294.1|CD981294
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|211499698|gb|FL406841.1|FL406841
EST:     TGCATGTATCAAAGCCTCCATAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32840746|gb|CD980427.1|CD980427
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|89252033|gb|DY623819.1|DY623819
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841252|gb|CD980933.1|CD980933
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32839985|gb|CD979666.1|CD979666
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32839499|gb|CD979180.1|CD979180
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32839696|gb|CD979377.1|CD979377
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32840986|gb|CD980667.1|CD980667
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841122|gb|CD980803.1|CD980803
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841145|gb|CD980826.1|CD980826
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|211532947|gb|FL381078.1|FL381078
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATCCCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32840104|gb|CD979785.1|CD979785
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32840762|gb|CD980443.1|CD980443
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32863734|gb|CF003416.1|CF003416
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841116|gb|CD980797.1|CD980797
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32841526|gb|CD981207.1|CD981207
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|32945502|gb|CF050321.1|CF050321
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTGTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
EST: gi|61119699|gb|DN560660.1|DN560660
EST:     TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAA                         GAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC
genomic: TGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCAC

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), 48 (downstream exon)
Score: 153

CTATGCAATTTGCTTGAACAGTGTTGGTTCCTGGAGCAATGACCTCTGGATGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 147

CTATGCAATTTGCTTGAACAGTGTTGGTTCCTGGAGCAATGACCTCTGGATGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

CTATGCAATTTGCTTGAACAGTGTTGGTTCCTGGAGCAATGACCTCTGGATGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 191

CTATGCAATTTGCTTGAACAGTGTTGGTTCCTGGAGCAATGACCTCTGGATGCATGTATCAAAGCCTCCAGAAAATCCCTATATCAAGCAAATCTTTGAAgtatgttaat ... ttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttatctgggtaatgatagtcatattgatatctgtgaatttatttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA
                        tattgat  putative branch site (score: 191)
                                            tttgctttc  putative PPT
                                      aatttatttgcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaatcatttgaagcttgttggtccttaacccttgttatctgggtaatgatagtcatattgatatctgtgaatttatttgctttcagGAATTTTCGGATGTCTCTAAAGAAATGGGTGTTTCAGTTGGAATCAAGCACAAGAAGATTAATGTCTCAAATCCTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG