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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctctccttttgaactccctctctcccccacctttagtgtcagtaatttgattgaattgcctcatatttcctttaaagatgaagcggtcctaatcatagtttctgtttgggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG

Basic information

species Zea mays
transcript GRMZM2G111579_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 9
--------gttagctctccttttgaactccctctctcccccacctttagtgtcagtaatttgattgaattgcctcatatt---------tcctttaaagatgaagcgg--------------------tcctaatcatagtttctgtttgggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG
         |    | || |      |  ||    |||||||||   |      | ||||||||||||   |||||| ||         |  |||| | |||||  |                     | || || ||||||| | | |  |  ||||||||||||| ||||||||||||||||||||| ||||| ||||||||||| || |||||||| ||||| |||||||| || |||||||| ||||||
gttagtatatataatttcataccattcgaccctcttcccccacccagaacactggcaatttgattgaag-acctcattttggccaaagatattttacacatgaaatgaaggtttccatgttactgaaattctgattatagtttgtttctttga-tgcagGTTTGAGCGATATGTGGACTATGCATTAGATGTCCCGATGTATTTTGTCTATCGAAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 9
-------gttagctctccttttgaactccctctctcccccacctttagtgtcagtaatttgattgaattgcctcatatt---------tcctttaaagatgaagcg--------------------gtcctaatcatagtttctgtttgggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG
         ||    || |      |  ||    |||||||||   |      | ||| ||||||||   |||||| ||         |  |||| | |||||  |                     | || || ||||||  | | |  |  ||||| ||||||| |||||||||||| ||||||||  |||| ||||||||||| || || ||||| ||||| |||||||| || |||||||| ||||||
gttagtatctataattcataccattcgaccctcttcccccacccagaacactggcaatgtgattgaaa-acctcattttggccaaagatattttatacatgaaatgaaggtttccatgtaactgaaattctgattatagttcgtttctttga-tgcagATTTGAGCGATATGTGGACTACGCATTAGATATCCCGATGTATTTTGTCTATCGTAATAAGAAGTACATTGACTGTACTGGAATGTCATTTCGG
















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|211306284|gb|FL001397.1|FL001397
EST:     GATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGG                         GTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTA
genomic: GATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTA
EST: gi|211304265|gb|FL001391.1|FL001391
EST:     GATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGG                         GTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTA
genomic: GATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTA

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: 69

CCATATCTGGACAGATACTGATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

CCATATCTGGACAGATACTGATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

CCATATCTGGACAGATACTGATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 16

CCATATCTGGACAGATACTGATAATAATCGTGCAGGGATGCTCCCTTTTGTCTTTGACGACTCATTTGGgttagctctc ... gggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttcctttaaagatgaagcggtcctaatcatagtttctgtttgggggtgcagGTTTGAGCAATATGTGGACTATGCATTAGAAGTCCCCATGTATTTTGTGTACCGAAATAAAAAGTATATTGACTGCACCGGAATGTCGTTTCGG
                        tcctaat  putative branch site (score: 16)
        tttaaagat  TA-rich tract