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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggtagtcatctgtaccctcctttgaactgtaccctttaggcctcatgtacttctctttgtttctcagacagtcttctatttgccttacgctgccaaacttttggacatgaaactaggcaactttaatgacaaattttgtactgtgtggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC

Basic information

species Zea mays
transcript AC148167.6_FGT001
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC148167.6_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g08790.1 (Oryza sativa), 3'ss of exon 2
gtctggtagtcatctgtaccctcctttgaactgtaccctttaggcctcatgtacttctctttgtttctcagacagtcttctatttgccttacgctgccaaacttttggacatgaaactaggcaactttaatgacaa-attttgtactgtgtggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC
                                                         |   ||    || |   | ||   ||   |  ||    |  |    | | || ||||||  || ||  | || |||||| |||||  |  ||   |  ||||||||||||||| | ||||||||||||||||| ||| ||||||  ||||| || ||||| || ||||| |||||||| || |||||   
---------------------------------------------------------tgactgcagttctgtttggctggcataaactgta----gtaagctctcttgagatgaaataagccagttctattgacaatattttccatggttatggattgcagAGTCCATCAGTGACACCCAGGAAGCCTCTGCAAGCTGACAGTACTTCCCATAGTCACGAAGATGATTCATATTCGGTTACTTC---
















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|149082930|gb|EE172164.2|EE172164
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|8103394|gb|AW928034.1|AW928034
EST:     AAAAACTTTCAGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTTACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|149099639|gb|EE185684.2|EE185684
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|149097420|gb|EE183276.2|EE183276
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|148968362|gb|EE019509.2|EE019509
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|148929700|gb|EC876422.2|EC876422
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|211410393|gb|FL027532.1|FL027532
EST:     GATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: GATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
EST: gi|8367407|gb|BE050352.1|BE050352
EST:     AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAG                         AGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC
genomic: AAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCAC

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: 252

ATCTGGAGCAGGGAATATTGCTCGAATTCCTCATCCCACCAGCAGCGGGGAAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 233

ATCTGGAGCAGGGAATATTGCTCGAATTCCTCATCCCACCAGCAGCGGGGAAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 221

ATCTGGAGCAGGGAATATTGCTCGAATTCCTCATCCCACCAGCAGCGGGGAAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

ATCTGGAGCAGGGAATATTGCTCGAATTCCTCATCCCACCAGCAGCGGGGAAAAACTTTCGGATAAAAGTAGCTCCTCACCAAGAAGCATGGCAAAGAAGgtctggtagt ... ggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacatgaaactaggcaactttaatgacaaattttgtactgtgtggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC
                   ctttaat  putative branch site (score: 514)
                    tttaatgacaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggtagtcatctgtaccctcctttgaactgtaccctttaggcctcatgtacttctctttgtttctcagacagtcttctatttgccttacgctgccaaacttttggacatgaaactaggcaactttaatgacaaattttgtactgtgtggatttgcagAGTCCATCATTCACACCCAGGAAGCCTCTCCAATCTGACAACACTTCTCACAGTCAAGATGATGACTCATATTCTGTCACTTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG