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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccttttggaacaagtgcctgcacctggccaggggaccactcgtttgtactcgtccgttaattctgcctctcttctcgttatgcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG

Basic information

species Zea mays
transcript GRMZM2G411333_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G411333_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 3
--------------------------------------------gtgagccttttggaacaagtgcctgcacctggccaggggaccactcgtttgtactcgtccgttaattctgcctctcttctc-gttatgcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG
                                               |      | | |   |||  || |  | |    |  |   ||  |     |    ||   |  |  |  ||||  ||| ||  || || ||||||||||||||| |||| |||||||||||||| || || |||| ||| || |||||||||||||| || || |||||| | ||||||||||| || ||| | 
gtgagccttttctcttctcaggcgaaaaaacgaaaagaaaaacaaaaaaaaaactagcatgtgtggatggaaatcggtgtgaaaaaccttctgaaagcgatgccaagatctgggggtctcccctctgtcgtgatt-tgcagGTGTGGTGCTAAGCTGGGTGGGGATTTGGGGTCGTCAAACCTGGCACTCGATGGGATTCTTGGATTTGGTCAGTCGAACTCGTCGATGCTGTCACAGCTC
















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|71443428|gb|DR824478.1|DR824478
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
EST: gi|71329431|gb|DR801432.1|DR801432
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGTGCTCAGCTTGGT
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGT
EST: gi|94472394|gb|EB701352.1|EB701352
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCCAGGCCCTTG
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACC-AGGCCCTTG
EST: gi|148946390|gb|EC891698.2|EC891698
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGGGCTCAGCT
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCT
EST: gi|31356527|gb|CD440884.1|CD440884
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
EST: gi|148962846|gb|EE013768.2|EE013768
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGT                         GTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
EST: gi|91048431|gb|EB158849.1|EB158849
EST:     GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGG                         GTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA
genomic: GTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGA

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), 45 (downstream exon)
Score: 16

GGAGCACAACCACCGGCTTCTACGTCACAGACTTCGTGCAGTACAACCAGGTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GGAGCACAACCACCGGCTTCTACGTCACAGACTTCGTGCAGTACAACCAGGTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GGAGCACAACCACCGGCTTCTACGTCACAGACTTCGTGCAGTACAACCAGGTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 61

GGAGCACAACCACCGGCTTCTACGTCACAGACTTCGTGCAGTACAACCAGGTGTCCGGCAACGGCCAGACCACCACGTCCAATGCCAGCATCACCTTTGGgtgagccttt ... gcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcgtttgtactcgtccgttaattctgcctctcttctcgttatgcttctgcagGTGTGGTGCTCAGCTTGGTGGGGATTTGGGATCCTCGAACCAGGCCCTTGATGGGATTCTTGGGTTCGGCCAGTCGGATTCGTCGATGCTATCGCAGTTG
                  cgttaat  putative branch site (score: 61)
                        ttctgcctctcttctc  CT-rich tract
                    ttaattct  TA-rich tract