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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctggttgctcaaactattgttttgtgctttgtttagtgatttccagttatttaatatcctcattttgtttttgctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG

Basic information

species Zea mays
transcript GRMZM2G023037_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023037_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g55080.1 (Oryza sativa), 3'ss of exon 6
gtacgttctggttgc-tcaaactattgttttgtgctttgtttagtgatttccagttatttaatatcctcattttgtttttgctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG
||  | | |   ||  || || |||   |||  || ||  | ||  ||||   | |  | |||| | |  |  | ||||     ||  ||||| ||||||||||| |||||||| ||| ||||| ||||||||||||||||| ||||||| ||| |||| ||||| |||||||| | ||||||||| ||||
gttagatatatctgtgtccaagtatc--tttaagcctt--tcagcaattttgtgctgataaatagcattgtcctttttt----gcttgtagGTACCTTTGTTTGAGAATATGGACGAAAGATTGCTGGATGCAATATGTGAGAGGTTAAGGCCTACACTATACACTGAAAATGAATACATTTTGAGAGAAG
















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|211219231|gb|FL262874.1|FL262874
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211219232|gb|FL262875.1|FL262875
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211221295|gb|FL262882.1|FL262882
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211221296|gb|FL262883.1|FL262883
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211221292|gb|FL262879.1|FL262879
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211221291|gb|FL262878.1|FL262878
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211219233|gb|FL262876.1|FL262876
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211219229|gb|FL262872.1|FL262872
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|7135191|gb|AW497976.1|AW497976
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211219228|gb|FL262871.1|FL262871
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211221290|gb|FL262877.1|FL262877
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
EST: gi|211219230|gb|FL262873.1|FL262873
EST:     ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGG                         GTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG
genomic: ATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAG

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), 37 (downstream exon)
Score: 14

GGAAACCAGGGGAGTAGACGAAGAAACTTTGGTTCAAACTCTTCCAAAAGATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG


Block sizes: 41 (upstream exon), 20 (downstream exon)
Score: 3

GGAAACCAGGGGAGTAGACGAAGAAACTTTGGTTCAAACTCTTCCAAAAGATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 15

GGAAACCAGGGGAGTAGACGAAGAAACTTTGGTTCAAACTCTTCCAAAAGATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 6

GGAAACCAGGGGAGTAGACGAAGAAACTTTGGTTCAAACTCTTCCAAAAGATCTTAGGAGGGATATCAAGCGGCATCTTTGTTTGGGCTTAGTGAAAAGGgtacgttctg ... ctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttagtgatttccagttatttaatatcctcattttgtttttgctactgatagGTGCCTTTGTTTGAAAATATGGATGAACGATTGTTGGATGCAATATGTGAGCGGTTAAGACCTGCACTCTACACAGAAAATGAGTTCATTTTGAGGGAAG
                    atttaat  putative branch site (score: 6)
                                       tttttgct  putative PPT
                agttatttaatat  TA-rich tract