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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgtcgcttccctgtgaaataactagcctgcatgctttctctgtaactattgacttaacactgtcttcaaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG

Basic information

species Zea mays
transcript GRMZM2G160504_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 12
gtaactgtcgcttccctgtgaaataactagcctgcatgctttctctgtaactattgacttaacactgtcttcaaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG
|||| |  | ||||||  |||||| ||     ||   |  || |||||||| ||    |    |||  ||| ||||  ||||| |||||  |||| ||||||||| |||||||||| || |||||||||||||||||  ||
gtaatttcctcttcccaatgaaatcacctttttgttag--ttgtctgtaacaataacatagtgactcacttaaaattgcagATCTCTACTGCTGGGATGACTCTAAGCCTTCTTGCAGTATCTGTTGTATTTTTTCTGGAG

upper sequence: GRMZM2G160504_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 12
gtaactgtcgcttccctgtgaa-ataactagcctgcatgct-ttctctgtaactattgacttaacactgtcttcaaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG
|||| | ||     ||||  |  | | |  ||     | || |  ||||| || ||  |   | | ||  |||||| |   |||| ||| |  |||| ||||||||| |||| ||||| ||| ||||||||||||| ||||||
gtaattctcttcctcctgaaactaaagcatgctaattttctgtattctgtgaccat-aataaagctctcgcttcaacttctagATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG
















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|19769428|gb|BQ034149.1|BQ034149
EST:     GAGCTGGACGACGCATCCTTCTCATT                         ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT
genomic: GAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT
EST: gi|78120836|gb|DV539220.1|DV539220
EST:     GAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATT                         ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT
genomic: GAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT
EST: gi|19769435|gb|BQ034156.1|BQ034156
EST:     CGCATCCTTCTCATT                         ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT
genomic: CGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTT

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: 15 (upstream exon), 46 (downstream exon)
Score: 4

GTCCTTGCTACTGGAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 44

GTCCTTGCTACTGGAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

GTCCTTGCTACTGGAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG


Block sizes: 40 (upstream exon), 45 (downstream exon)
Score: 70

GTCCTTGCTACTGGAGTTACAACATGGCTGTTAGACCGAGCTGGACGACGCATCCTTCTCATTgtaactgtcg ... caaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcctgcatgctttctctgtaactattgacttaacactgtcttcaaatgacagATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG
                                      ctgtcttc  CT-rich tract
                     taactatt  TA-rich tract