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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttttcactgctctgtggatgttattacagtcttcatttcggctcagggtcacgcagattataaatatttattgacttttggtttgacattgttcag

Basic information

species Zea mays
transcript GRMZM2G030072_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030072_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g22430.1 (Oryza sativa), 5'ss of exon 9
-GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagt--tttttcactgctctgtggatgttattacagtcttcatttcggctcagggtcacgcagattataaatatttattgacttttggtttgacattgttcag
 ||||||||||||||||||||||||||| || |||||||||||||| ||||||||||  |||||| | |||| ||||| | |||||||| || || ||| ||||||   |  | |  || ||||| ||| | ||           ||| |  | | |  ||      ||||  |||| | | |  |  |  ||| |   ||| |||
AGTACATGGCTGACATGCTCTCCCCAGAGGAATGGGACAAAGTTGCTGGAGTCAGACGCCCTGATATTATGTGATGTTGTACATTGAAATTTTAA-ATTAGgtaagatatcctccgttgttctgtagat-tgat----------gtttggaattatgaacat-----ttattcatatatttggtttgatacttttatgatgtgcag
















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|67030852|gb|CO459601.1|CO459601
EST:     TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTG                         GTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|9255042|gb|BE345510.1|BE345510
EST:     TCAGACATCCTGATCTAATGTGATGTTATTCATTGAAAGTTCAACA--T-                         -TT-GGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|211175971|gb|FL481231.1|FL481231
EST:     TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTG                         GTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|60355320|gb|DN222293.1|DN222293
EST:     TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTG                         GTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|56382319|gb|CV984988.1|CV984988
EST:     TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTG                         GTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|16926968|gb|BM080036.1|BM080036
EST:     TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTG                         GTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|9255043|gb|BE345511.1|BE345511
EST:     TTAGACATCCTGATCTAATGTGATGTTATTCATTGAAAGTTCAACATTTG                         GTTA----A-TAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
EST: gi|9824865|gb|BE575172.1|BE575172
EST:     TCAGACATCCTGATCTAATGTGATGTTATTCATTGAAAGTTCAACA--T-                         -TT-GGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT
genomic: TCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAAT

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), 45 (downstream exon)
Score: 28

GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAATGCTTGATTATCAATGATAATGGTTGGTAAGAGCCAAGGAGTACTTGTTT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 66

GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAATGCTTGATTATCAATGATAATGGTTGGTAAGAGCCAAGGAGTACTTGTTT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 26

GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAATGCTTGATTATCAATGATAATGGTTGGTAAGAGCCAAGGAGTACTTGTTT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 18

GTACATGGCTGACATGCTCTCCCCAGATGAGTGGGACAAAGTTGCCGGAGTCAGACATCCTGATCTAATGTAATGTTATTCATTGAAAGTTCAACATTTGgtaagttttt ... cattgttcagGTTAGGTTAATAGCTTCCAGGGGGCAGAAACAGGTGACGCTGAACAATAATGCTTGATTATCAATGATAATGGTTGGTAAGAGCCAAGGAGTACTTGTTT