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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttattttcatcaacactacactgcaactttgagatcctctccttgtgagctgttcatgctatggccagttcagctaaacgccgccgtgtccgtgtcttgttttttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT

Basic information

species Zea mays
transcript GRMZM2G088964_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088964_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g27580.1 (Oryza sativa), 3'ss of exon 5
gttgtttattttcatcaacactacactgcaactttgagatcctctccttgtgagctgttcatgctatggccagttcagctaaacgccgccgtgtccgtgtcttg--ttttttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT
                                     | |  | || ||| ||   || ||| ||     || || |  || |||      | ||      |||   ||||| |||||||||||||||||||||||||||||| |||||| |||||||||| || |||||||||||||| ||||| || ||||| ||||| |||||  |||| || ||||
-------------------------------------gttagtttcattgaga--cgtccat-ctg----caattta--tacacgatataatttcttacagttgatcttttttttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGGGCAAACAGCATACCTTATAAACAATGTCAATGACTTTGGTGATGGTTTCT
















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|74243893|gb|DT651807.1|DT651807
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|71442520|gb|DR823570.1|DR823570
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|50330411|gb|CO525537.1|CO525537
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|88757480|gb|DY541621.1|DY541621
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|76288735|gb|DV028303.1|DV028303
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|76936790|gb|DV174895.1|DV174895
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|76283777|gb|DV023345.1|DV023345
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
EST: gi|50333421|gb|CO528547.1|CO528547
EST:     CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAG                         ATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG
genomic: CTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGG

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 3 RNA-Seq libraries.


Block sizes: 30 (upstream exon), 24 (downstream exon)
Score: 3

GCGCTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT


Block sizes: 35 (upstream exon), 26 (downstream exon)
Score: 2

GCGCTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT


Block sizes: 40 (upstream exon), 44 (downstream exon)
Score: 11

GCGCTGAAGCCATGTTTGCAGACCTTGGCCACTTCAGTAAGAAGGGTATTCAGgttgtttatt ... ttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatggccagttcagctaaacgccgccgtgtccgtgtcttgttttttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT
             agctaaa  putative branch site (score: 11)
                                    tcttgttttttgtttt  putative PPT
                                      ttgttttttgtttt  TA-rich tract