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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagaacatgtccctgctgcgtgcgaagggaggaggcaggctcctgactcctctccattttattttatcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 10
-----------gtgagcagaaca-tgtccctgctgcgtgcgaagggag---gaggcaggctcctgactcctc--tccattttattttatcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG
           ||    || ||| |       ||| ||||  |    |    | |   ||||     ||||   | |   || ||  ||| |  ||||| ||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||| |||| || |||||||
gtgagtaatttgttgataggacagtaatttaactgtgtgcagatcatgcccaatgttagctcagttttcctgaattctcctttttccatctggcgcagGAAAATTTGGAGCATTGTTTGCTTCCATCCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG

upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 11
-----------gtgagcagaaca-tgtccctgctgcgtgcgaagggag---gaggcaggctcctgactcctc--tccattttattttatcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG----------------------
           ||    || ||| |       ||| ||||  |    |    | |   ||||     ||||   | |   || ||  ||| |  ||||| ||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||| |||| || |||||||                      
gtgagtaatttgttgataggacagtaatttaactgtgtgcagatcatgcccaatgttagctcagttttcctgaattctcctttttccatctggcgcagGAAAATTTGGAGCATTGTTTGCTTCCATCCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGGTTGGTTACCCTGCGCCATCTG
















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|91049744|gb|EB160162.1|EB160162
EST:     ATGATC-TTTTCTCCATGCTGG                         GGAAATTTGGAGCGTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|149071735|gb|EE160128.2|EE160128
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|71759661|gb|DR957598.1|DR957598
EST:     CGGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: C-GGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|74238881|gb|DT646795.1|DT646795
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|50337438|gb|CO532564.1|CO532564
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|211379070|gb|FL028411.1|FL028411
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATATTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|166597529|gb|EG272921.1|EG272921
EST:     CGGGTCATACAGATCTCAGCTAGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCG
genomic: CGGGTCATACAGATCTCAGCT-GGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCG
EST: gi|76287139|gb|DV026707.1|DV026707
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|76287138|gb|DV026706.1|DV026706
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
EST: gi|71310985|gb|DR791794.1|DR791794
EST:     ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGG                         GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG
genomic: ACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCG

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: 48 (upstream exon), 49 (downstream exon)
Score: 112

GGAGAACGTCGGGTTGCTTGGGTCGACAAGGATCGGGAGCCGACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 19

GGAGAACGTCGGGTTGCTTGGGTCGACAAGGATCGGGAGCCGACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 10

GGAGAACGTCGGGTTGCTTGGGTCGACAAGGATCGGGAGCCGACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG


Block sizes: 32 (upstream exon), 42 (downstream exon)
Score: 2

GGAGAACGTCGGGTTGCTTGGGTCGACAAGGATCGGGAGCCGACGGGTCATACAGATCTCAGCTGGCTTCATGATCTTTTTCTCCATGCTGGgtgagcagaa ... tcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgaagggaggaggcaggctcctgactcctctccattttattttatcggttgcagGGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG
                   tcctgac  putative branch site (score: 2)
                         ctcctctccattttat  CT-rich tract
                               tccattttattttat  TA-rich tract