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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattctttttcctcatcgagctctactgtacctttctcctaacagtgccgaaggctacgatatatgttttctcctaacaattttcatcattactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 3'ss of exon 6
gttattctttttcctcatcgagctctactgtacctttctcctaacagtgccgaaggctacgatatatgttttctcctaacaattttcatcattactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG
|| | ||  | |   ||| || |||| || |   ||| |||||| |     |     |||||||  | |||  |   |  |||||  ||  ||  |    ||||||||||||  |||||||| || ||||| ||||| ||| | |||||||||||||
gtcactccctattgacattgaactctgctatgagttt-tcctaataagcatg-----tacgata-gtatttgttgtcattaatttg-atgttt--tgaacagGCTGGTAGAGGTCTTTTCCTCCTCCTCTCGAGATTTATGCTGTTCTATGATCAAG
















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|71430125|gb|DR811175.1|DR811175
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|13381878|gb|BG458553.1|BG458553
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTC
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTC
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAG                         GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT
genomic: TTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGAT

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), 46 (downstream exon)
Score: 39

TATCTCCTTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 35

TATCTCCTTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 24

TATCTCCTTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 40

TATCTCCTTGAGGACGTTGCTCTAGTCCCTGAAAGACTTAGTAAAATATCATTACAGgttattcttt ... tactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccgaaggctacgatatatgttttctcctaacaattttcatcattactctgtagGCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG
                          tcctaac  putative branch site (score: 40)
                                            ttactct  putative PPT
                                 aattttcatcatta  TA-rich tract