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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcttttctgattttctttctgtttttcacataagtgagctgtaactattgtctacttgactttaaacttacgaggtgatatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG

Basic information

species Zea mays
transcript GRMZM2G146794_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146794_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g14120.1 (Oryza sativa), 3'ss of exon 5
gtatgtttcttttc--tgattttctttctgtttttcac-ataagtgagctgtaactattgtctacttgactttaaacttacgaggtgatat-gtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG
|||||| |||||||     |||   |||| | ||     |||| ||   ||||   |     |  |||| ||| | |  ||  ||  | || |||||||||| || |||| ||| ||||| || ||||| ||||||||||||||||||||||| |||||
gtatgtctcttttcaccactttatattctctcttctgttataaatgttgtgtataaacgtaattattgatttttacccaacatgggaaaattgtttcagTGATTTATCATCCAATAATTTGAGCGGCCCGGTTCCAAAAATCTATGCACATGACTACAG
















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|89756132|gb|DY686285.1|DY686285
EST:     TCTGGGCCGATCCCAACAGATGTCGCTAGGCTTCCAGGTCTCACATTCCT                         TGACTTGTCATTCAACAATTTAAGTGGCCCCAGT-CCAAAAATCTATGCAC
genomic: TCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCC-AGTTCCAAAAATCTATGCAC
EST: gi|166409995|gb|EG133125.1|EG133125
EST:     CTGGGCCGATCCCAACAGATGTTGCTAGGCTTTCCAGGTCTCACATTCCT                         TGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTA
genomic: CTGGGCCGATCCCAACAGATGTTGCTAGGC-TTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTA
EST: gi|91872683|gb|EB402640.1|EB402640
EST:     TCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCT                         TGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACA
genomic: TCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACA

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: 44 (upstream exon), 39 (downstream exon)
Score: 45

ACGCCTTGATAGGAATAACTTGTCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 12

ACGCCTTGATAGGAATAACTTGTCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 20

ACGCCTTGATAGGAATAACTTGTCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

ACGCCTTGATAGGAATAACTTGTCTGGGCCGATCCCAACAGATGTTGCTAGGCTTCCAGGTCTCACATTCCTgtatgtttct ... tatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagctgtaactattgtctacttgactttaaacttacgaggtgatatgtttcagTGACTTGTCATTCAACAATTTAAGTGGCCCAGTTCCAAAAATCTATGCACATGATTACAG
                               aacttac  putative branch site (score: 25)
                           tttaaactta  TA-rich tract