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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcacatttcatactccaatccaatgttgagtctgataaaagtattcagcgtggtcttaatgtaaaggaaaagaaaacatgatccttcgtacatgtcagaaacaggaaaatcagaaaaggcttatcagtgtaataatgcagcttccttatgaatattgatcatcactaacacagtccctacttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT

Basic information

species Zea mays
transcript GRMZM2G110735_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 3
gttagcacatttcatactccaatccaatgttgagtctgataaaagtattcagcgtggtcttaatgtaaaggaaaagaaaacatgatccttcgtacatgtcagaaacaggaaaatcagaaaaggcttatcagtgtaataatgcagcttccttatgaatattgatcatcactaacacagtccctacttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT
                                                                                             |    |   | | || |   |    || ||  ||    |  |||| ||||||     | |||   |    || | ||||||  ||  |||||| || | |||||||||| ||||||||||| || ||||||||||| || || |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |
------------------------------------------------------------------------------------------aaaatgatttgcatagagaagggtggttaatggtatac---ttcaatactgcagcgatactgtgatagtgatccacctctaacattgtttctactttattc-agGTTCTTCTGAGCAGGTTGCGGCTTTTCCTAAGTCCTGGATATCCTTACGAAGAAATACTGAGAACATTTCACAACCAAACAGACAATGTTATGTGCTCGT
















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|23199797|gb|BU582362.1|BU582362
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
EST: gi|67022056|gb|CO450805.1|CO450805
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
EST: gi|40336598|gb|CK370668.1|CK370668
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
EST: gi|211210848|gb|FL335709.1|FL335709
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGAGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
EST: gi|21891489|gb|BQ744702.1|BQ744702
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
EST: gi|32832826|gb|CD972504.1|CD972504
EST:     GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGT
genomic: GTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGT
EST: gi|23357502|gb|BU645151.1|BU645151
EST:     TCCAAACTATGGAGTATTTACCCTGGGATGACAAACTTCCAGGAGCTCAG                         GTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA
genomic: TCCAAACTATGGAGTATTTA-CCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAA

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: 255

CGCCACAGCCCCAGGAATGGCGAAGCATGCTGGAGCCTACTGGTTTGGAAGTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 689

CGCCACAGCCCCAGGAATGGCGAAGCATGCTGGAGCCTACTGGTTTGGAAGTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 481

CGCCACAGCCCCAGGAATGGCGAAGCATGCTGGAGCCTACTGGTTTGGAAGTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2344

CGCCACAGCCCCAGGAATGGCGAAGCATGCTGGAGCCTACTGGTTTGGAAGTCCAAACTATGGAGTATTTACCTGGGATGACAAACTTCCAGGAGCTCAGgttagcacat ... ttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagcttccttatgaatattgatcatcactaacacagtccctacttcatcccagGTTCTTCTCAGCAGGTTGCGACTCTTCCTAAGTCCAGGGTACCCTTACGAAGAAATACTGAGGACATTCCACAACCAAACCGACAATGTTATGTGCTCAT
                           cactaac  putative branch site (score: 2344)
                                      tccctacttcatccc  putative PPT
          ttatgaatattgat  TA-rich tract