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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatatttatactcaactagcgatattaatgttctgattatatctgttgtgttagtgatatatatcttaccttattgacaaattgtgattaaaataatgacag

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 5'ss of exon 10
GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatatttatactcaactagcgatattaatgttctgattatatctgttgtgttagtgatatatatcttaccttattgac-aaattgtgattaaaataatgacag
||||||| || ||||| || |||||||||||||| || ||||| || |||||||||||||| |||| | |||| || |||||| |   || |  |   | |        || | |   || |       |||  |||| |  | | |  || ||  || || |||||||   |       ||    
GACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATGgtaacccttgtttt--gccattttccaaaaagctggaatcaacatcagtgttgtagttac-tgtgttatagctctttaacgaaattgtttattctcccttgga--

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 5'ss of exon 10
GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatat----ttatactcaactagc-------gatattaatgttctgattatat-ctgttgtgttagtgatatatatcttacc-ttattgacaaat-tgtgattaaaataatgacag------------------------------------------------------------------------
||||||| ||||||||||| ||||| ||||| || || ||||| || || ||||||||||| |||| | |||| ||||||||| || |    || | ||  | ||||        | ||||||  | |||   ||| ||| | | | |  ||  | |||  | |  | ||  |  ||| |   | ||| | | ||   |                                                                        
GACGTGGAGCTAAGGAAGCCAATCTCTACACCGAGATAGCTGAAGGCATTCATGCTTATGGAATAAAAGGCCACCGGCATGgtaattttgtttttttctagattagctgaaatcaacattaattatgtgaccttatactgctctttaacagaattttattctcctgtgataaatgaatatactaataatagagtgtttgcttatatttatcttgttagttacctttaaggtagcctttctttattaacacaatgtgataaaaccatgccag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 5'ss of exon 9
GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatatttatactcaact-agcgatattaatgttctgattatatctgttgtgttagtgatatatatcttaccttattgacaaattgtgattaaaataatgacag
| ||||| || ||||| |||||||| ||||||||||| ||||| || || ||| ||||||| || ||||| ||||| |||||| | |||| |    | |  |  |||||||   |   |   |   |   | | ||    ||   | |||| || | |  |   ||  |  ||    | ||||   
GTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATGgtaagattt-tgtaaatcagaatgatattacaatgaagcaaaatccctatctatttacaattattttctttccatttaaattcataatattttt--tcatgat--

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|31354246|gb|CD438603.1|CD438603
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|6448353|gb|AW181119.1|AW181119
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATACCAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|110202395|gb|EC884292.1|EC884292
EST:     GGATAACAAGCCATCGGGCATG                         TGCCTGAGATTGAGCAAGGGCTTACAGATGCTGGGGAATCAAAAGTTACT
genomic: GGATAACAAGCCATC-GGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACT
EST: gi|71762552|gb|DR960489.1|DR960489
EST:     TGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|148958090|gb|EC904281.2|EC904281
EST:     GGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: GGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|74234670|gb|DT642584.1|DT642584
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|33093061|gb|CF053055.1|CF053055
EST:     GAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: GAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|32931562|gb|CF036374.1|CF036374
EST:     GAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: GAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|78080159|gb|DV508571.1|DV508571
EST:     CAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: CAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|22473066|gb|BU037546.1|BU037546
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGG-ATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG                         TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA
genomic: TGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTA

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), 49 (downstream exon)
Score: 220

GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 132

GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 124

GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 66

GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATGgtgatattta ... ataatgacagTGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG