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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgccttcagtgacttaacgatatcacagtattaaaatttataactttatgattca...

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g32610.4 (Oryza sativa), 5'ss of exon 12
GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgccttca-gtgacttaacgatatcacagtattaaaatttataactttatgattca---
|| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||    |||    ||    |||| |  |  ||    |   | |||  ||||  | |||    |   |     |  | |  |||   ||||| |  ||     
GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatccttt----tacccattttgccatattttaagacctgtttgatttcacattactctttgtggtactttttgttattttttctactttgtttttggaca

upper sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 11
GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgcct------tcagtgacttaacgatatcacagtattaaaatttataactttatgattca---
|| || || ||||| ||||||||||| || |||||||| || || || || ||| | ||||| |||||||| |||||||||||||| ||||| ||||| ||| ||       |  ||  |||   ||| ||  ||  | | |  | | |      ||| ||   || |   | |  ||| ||      |   ||||| || ||     
GCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAGgtaagag-----tggaatatcttgagcttgca--agatagacgtctacttcgataatcaatgttctagc--caccttagttttgctgccttgcactttttgttttgatt
















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|20802940|gb|BQ293990.1|BQ293990
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     TTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: TTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     GGGATCTTGAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC

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: 49 (upstream exon), 48 (downstream exon)
Score: 71

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


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

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT