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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatgtttctgatggcactagccaataatcgtagttttggctactactagttgagtatgtgcgacatgacagattgtgttccacattagttaaagaaaaagacatagaagatgtttttgcttttcctctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 9
gtttgtatgtttctgatggcactagccaataatcgtagttttggctactactagttgagtatgtgcgacatgacagattgtgttccacattagttaaagaaaaagacatagaagatgtttttgcttttcctctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT
||| ||||| |  || ||    |   |  |     || |  |  || || |||  ||  | || |     ||   ||| |  |  |   || |    |   | ||    ||          | |||    | | |||  |||||| ||||  || ||| |||     ||||||| |    ||||||||||||||| |||||||||||||  |||| || ||  | ||||||||||| ||||||||||||| |||||||||||||||  |||| ||  |||||||||
gttagtatgctattgttgtt-ttgttctgtgg--atactaataact-ctcctacctgcttgtg-gttgtgtg---gatggcctagcttgttgggccgaatcataggtccag----------tccttcaagtttcctcagttttggtcaatt-tacagtcataa----cctttggtgctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT
















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|33104324|gb|CF064284.1|CF064284
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCGTATCTCAATTGACATCTGGAAAGCAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|211453990|gb|FL038183.1|FL038183
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCGTATCTCAATTGACATCTGGAAAGCAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|19436236|gb|BM952646.1|BM952646
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|211453987|gb|FL038180.1|FL038180
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACC
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACC
EST: gi|213179269|gb|FM196444.1|FM196444
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|9732140|gb|BE510892.1|BE510892
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCGTATCTCAATTGACATCTGGAAAGCAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|22490101|gb|BU050024.1|BU050024
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|19351144|gb|BM895676.1|BM895676
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|33101745|gb|CF061705.1|CF061705
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCGTATCTCAATTGACATCTGGAAAGCAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|18655285|gb|BM500090.1|BM500090
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|60358249|gb|DN225222.1|DN225222
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCGTATCTCAATTGACATCTGGAAAGCAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
EST: gi|87153521|gb|DY398310.1|DY398310
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAG                         GTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAA

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), 49 (downstream exon)
Score: 189

CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 536

CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 797

CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 847

CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgt ... gaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcagGTTGCAAGGATTCTAATGAAGACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAAT
                aatgatatagtaata  TA-rich tract