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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcccttttcgttgctcccagtcccatccaatacattactgtgccgttaacatggagcgcgcgcatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatcgtcgatgaatttccttttttctttaattaattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG

Basic information

species Zea mays
transcript GRMZM5G885392_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 6
gtattttcccttttcgttgctcccagtcccatccaatacattactgtgccgttaacatggagcgcgcgcatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatcgtcgatgaatttccttttttctttaattaattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG
                                                                                            ||| |  ||     |||  ||| ||   |    || | ||  ||| ||  |  || |  |   ||| || |  ||| |   |||| ||||| || ||||| || |||||||| || |||||||| || || |||||||| ||||||||||||||  ||| |||||| ||||||||||||| 
-------------------------------------------------------------------------------------------gtattttcattgtcttat-catacat-cgtgggcatgt-taagtatggt--acaaaatgacaaattttttga--taact---agGGACCGTGCCCGAACTGTGGCAATGAAAATCTTTCCTTCTTTGGGACTATACTGTCTGTGCCTAGCGGTGGTGCAAGAAACAGTGTGAAATGTGCAAA
















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|18178811|gb|BM380021.1|BM380021
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|88748429|gb|DY532570.1|DY532570
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTTTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|32924858|gb|CF029670.1|CF029670
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
EST: gi|71760700|gb|DR958637.1|DR958637
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|32925008|gb|CF029820.1|CF029820
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
EST: gi|32926006|gb|CF030818.1|CF030818
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCCTCTTCGGTACC
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACC
EST: gi|86468794|gb|DY235164.1|DY235164
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|6827379|gb|AW331022.1|AW331022
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGCAACGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|32926318|gb|CF031130.1|CF031130
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGT
EST: gi|78074964|gb|DV503398.1|DV503398
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|13381842|gb|BG458517.1|BG458517
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|148942558|gb|EC887577.2|EC887577
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTTTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|32942294|gb|CF047113.1|CF047113
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTA
EST: gi|211475315|gb|FL222267.1|FL222267
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|110538710|gb|EE042664.1|EE042664
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTTTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA
EST: gi|211475316|gb|FL222268.1|FL222268
EST:     TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAG                         GGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTCCTTCGGTACCATA
genomic: TAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATA

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: 44 (upstream exon), 39 (downstream exon)
Score: 3

TTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 8

TTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 126

TTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCCTGATCTTGAAGgtattttccc ... taattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatatatatatatcgtcgatgaatttccttttttctttaattaattttcagGGTCCGTGTCCAAACTGCGGGAATGAAAACCTCTCCTTCTTCGGTACCATACTGTCAGTGCCTAGCGGTGGCTCAAAAAACAGCGTGAAATGTGCAAG
                                          aattaat  putative branch site (score: 126)
                           tttccttttttcttta  CT-rich tract
                      atgaatttcctttttt  TA-rich tract