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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgtctcttataatttgacttttctatataagggggagctctaaatcatcattttcatgtttaagatataatgtttgcgtttctgttctattgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG

Basic information

species Zea mays
transcript GRMZM2G349603_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G349603_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g58390.1 (Oryza sativa), 3'ss of exon 2
ccgtctcttataatttgacttttctatataaggg-ggagctctaaatcat-cattttca---tgtttaagatataatgtttgcgtttctgttctattgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG
     | ||||  ||    ||  || | | |||  | |||| | | |    ||| |  |   |  |   ||||   |||||  |  |||  |||  || |||||||||||||||| || ||||||  |||||  |||||||||||||||||||||||||||||||||||||||||  ||
-----tattatctttcttgttgactgtgtgaggctgtagctttgatttgcacatataaaagataatggggatactctgtttatgcatcttctctgctggttgcagATATAAAGAAGCCTGGTGGAGAAGCTAAGGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTTCTG
















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|101383842|gb|EB813976.1|EB813976
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGGCATG                     
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGAT----CA-Ggcatggcaag ... ttgatt
EST: gi|149027791|gb|EE286087.2|EE286087
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|149027791|gb|EE286087.2|EE286087
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|149027791|gb|EE286087.2|EE286087
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|110937499|gb|EE157656.1|EE157656
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         ATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTT
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTT
EST: gi|89757701|gb|DY687191.1|DY687191
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|89757701|gb|DY687191.1|DY687191
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|89757701|gb|DY687191.1|DY687191
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166014|gb|FL265148.1|FL265148
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166014|gb|FL265148.1|FL265148
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166014|gb|FL265148.1|FL265148
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166007|gb|FL265141.1|FL265141
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166007|gb|FL265141.1|FL265141
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166007|gb|FL265141.1|FL265141
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|50336777|gb|CO531903.1|CO531903
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|50336777|gb|CO531903.1|CO531903
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|50336777|gb|CO531903.1|CO531903
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|14203984|gb|BG837661.1|BG837661
EST:     GTGGATGCGAGGGCGATCGAAGCGGTCATCGAGGGGGTTCATGTGATCAGGCATG                     
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGAT----CA-Ggcatggcaag ... ttgatt
EST: gi|149063787|gb|EE157657.2|EE157657
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         ATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTT
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTT
EST: gi|67014746|gb|CO443495.1|CO443495
EST:     GTGGATGCGAGGGCGATCGAAGCGGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|67014746|gb|CO443495.1|CO443495
EST:     GTGGATGCGAGGGCGATCGAAGCGGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|67014746|gb|CO443495.1|CO443495
EST:     GTGGATGCGAGGGCGATCGAAGCGGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|76936467|gb|DV174741.1|DV174741
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|76936467|gb|DV174741.1|DV174741
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|76936467|gb|DV174741.1|DV174741
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166009|gb|FL265143.1|FL265143
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166009|gb|FL265143.1|FL265143
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|211166009|gb|FL265143.1|FL265143
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|148931938|gb|EC875168.2|EC875168
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|148931938|gb|EC875168.2|EC875168
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-
EST: gi|148931938|gb|EC875168.2|EC875168
EST:     GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAG                         G
genomic: GTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcag-

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: 42 (upstream exon), 49 (downstream exon)
Score: 5

GGTTGACGGAGTATGATCCGGACGGGGTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 8

GGTTGACGGAGTATGATCCGGACGGGGTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 18

GGTTGACGGAGTATGATCCGGACGGGGTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 6

GGTTGACGGAGTATGATCCGGACGGGGTGGATGCGAGGGCGATCGAAGCTGTCATCGAGGGGGTTCATGTGATCAGgcatggcaag ... ttgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcattttcatgtttaagatataatgtttgcgtttctgttctattgattgcagATATAAAGAAACCAGGTGGACTAGCTACTGAAATAGAGAGTTACTTTGGTTGTTCAGCCTCAAATCTTGTGTTG
                                           tattgat  putative branch site (score: 6)
                                        ttctatt  CT-rich tract
     attttcatgtttaaga  TA-rich tract