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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttcatttatcctgcagtcgcaaactgaaataactcttttgtgttcttgatattatcttgttctcgtcaggttatctctatgatttcatgacatt...

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 8
GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaattt---catttatcctgcagtcgcaaactgaaataactcttttgtgtt--cttgatattatcttgttctcgtcaggttatctctatgatttcatgacatt
|| ||||||||||||||||||||||| || || |||||||||||||||   || ||||||||||| || ||||||||||| ||||| || ||||| |  ||   |  || | ||||||| |    |  | ||  ||||    | ||  | || || || ||   |  |      ||    |    |||  |  |    
GTGATCAGTGGTCACTTGGGATGGGTGCGGTCAATTGCATTTGATCCAAGTAACGAATGGTTCTGTACGGGTTCTGCCGACAGGACGATTAAGgtgagcttgctctcttcttctgcagtagtgttccaatatg-ctctgggatttttacatgttactagctgaatgcccgtgctttgcgacaggaattaaaaaa----

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G04910.1 (Glycine max), 5'ss of exon 7
GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgta---aatttca---tttatcctgcagtcgcaaactgaaataactcttttgtgttcttgatattatcttgttctcgtcaggttatctctatgatttcatgacatt
|||||||| |||||||||||||||||  ||||| ||||| |||||||    ||   |||||| || ||||||||||| ||| | || || ||||||    ||  ||   |  ||     ||| ||    |   | ||  | | | | |       |  || | |||   | || |||       |||||  |||     
GTCATCAGCGGTCACTTGGGATGGGTGAGATCTGTTGCAGTTGATCCCAGTAACACATGGTTTTGTACTGGTTCTGCAGATCGAACTATCAAGgtatttgatcacaaaatgcatgtcatagttgcttgttatgaaaaggcatatttataagaacaaaaatttagtt--ggccatgttgaactgttgattctatgg----
















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|78085590|gb|DV513983.1|DV513983
EST:     ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAG                         ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
genomic: ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
EST: gi|6021220|gb|AW066148.1|AW066148
EST:     ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAG                         ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
genomic: ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
EST: gi|32933221|gb|CF038033.1|CF038033
EST:     ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAG                         ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
genomic: ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
EST: gi|94478034|gb|EB706992.1|EB706992
EST:     ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAG                         ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
genomic: ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT
EST: gi|148962621|gb|EE013511.2|EE013511
EST:     ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAG                         ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGCCATATT
genomic: ATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATT

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: 260

GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 113

GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 111

GTCATCAGTGGTCACTTGGGATGGGTTCGATCTATTGCATTTGATCCAGCGAATGAATGGTTCTGCACTGGTTCTGCCGATAGGACAATAAAGgtaaatttca ... cttgctgtagATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG