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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcacagtccaattgacattctattcttccttgaatttattatcttagcatggcagtattaaagccagacattaattatgttactttttctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA

Basic information

species Zea mays
transcript GRMZM2G011575_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011575_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 1
gttcacagtccaattgacat-tctattcttccttgaatttattatcttagcatggcagtattaaagccagacattaa--ttatgttactttttctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA
  |  || | || || |  |  ||  | || || | |||| || |||  | || | || || |||   | || || |  ||||  |||||| | | |  |||||||||||||||||||| ||| ||||||||||||||||||||  ||||||| ||||||||||||||||||||||||| |||||| ||| |||||||  |||
--tttcatttcatttaatgtgcctcctgtttctgggatttcttctctaggtataggagaatgaaaataacactttgactttatactactttgtttttt-tcagGACAAGATGATGCTTCGACCAGCTGAGCGTTTAGTTGCATTCACAATTCTTCATCAAGGTTATTCCTCACAGTTGGAAAATCCCTTTGTTCCTCTAATAA
















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|91048056|gb|EB158474.1|EB158474
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|71307834|gb|DR790138.1|DR790138
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|211502396|gb|FK960896.1|FK960896
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|29167999|gb|CB411259.1|CB411259
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTTCTTTTT                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|31358140|gb|CD442497.1|CD442497
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|211502392|gb|FK960892.1|FK960892
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|148933022|gb|EE285909.2|EE285909
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA

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: 85

CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 42

CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 51

CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcatggcagtattaaagccagacattaattatgttactttttctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTACATCAAGGTTATTCCTCACAGTTGGCAAATCCATTTCTTCCTCTTTTAA
                         cattaat  putative branch site (score: 51)
                                  tgttactttttctct  putative PPT
                        acattaattatgttac  TA-rich tract