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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttatcttctctgtttttcccacagatttcctgtggttacatttacatatccatctgggcagcaaacttagaactaaacacatttttgttaaaatgattttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG

Basic information

species Zea mays
transcript GRMZM2G151916_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 7
gttagtttatcttctctgtttttcccacagatttcctgtggttacatttacatatccatctgg--gcagcaaacttagaactaaacacatttttgttaaaatgattttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
                | |||            | || ||  |   |||   ||||    ||     ||||||||| ||||||||||  |||||  |      |||||  ||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||||
--------------gttatttcctgtttgtggcttctttgactgtttttttttatcaggttgactatagcaaactttgaactaaacatcttttttgt----ccatttttccagCCTCTCTTTCCTGGTGAAAGTGCAGTGGATCAGCTTGTCGAGATTATAAAG
















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|32908149|gb|CF012962.1|CF012962
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTTCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|31363416|gb|CD447773.1|CD447773
EST:     ATATTT-GTCAGCTGGATGTG-TCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTTTCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: ATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|60398307|gb|DN231123.1|DN231123
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|211015494|gb|FL335940.1|FL335940
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTTCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|211033507|gb|FL333369.1|FL333369
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|91875587|gb|EB405544.1|EB405544
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
EST: gi|211159258|gb|FL355922.1|FL355922
EST:     TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAG                         CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
genomic: TTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG

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: 174

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACCGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 126

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACCGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 178

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACCGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

TTACCGTGCTCCAGAGCTCATATTTGGGGCAACCGAGTACACAACATCAATTGATATTTGGTCAGCTGGATGTGTTCTTGCTGAGCTGCTTCTTGGCCAGgttagtttat ... attttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctgggcagcaaacttagaactaaacacatttttgttaaaatgattttatcagCCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG
                    aactaaa  putative branch site (score: 121)
                                              ttttatc  putative PPT
                       taaacacatttttgtt  TA-rich tract