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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggttttcactatgctgaattgtatccaatgtttaaatgttcaatgttctagctgacagtgacttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 5
gtac-tggttttcactatgctgaattgtatccaatgtttaaatgttcaatgttctagctgacagtgacttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT
|||| || ||| | ||   |||| || | ||  || | |||   || |    |||| || ||| || |||| ||||||||||||||||||||||||| ||||||||||  |||||||||||||| || ||||| ||||||||||||||||||||||| |||
gtacgtgatttacgctgcactgagttatgtcagatatgtaatatttta----tctacctaacactg-cttgtaacagGTGAAACTGATTGACTTCTCCCCTGGTGAGAAATATTTGGTCACATATAGTAGCCACGAGCCCAGCAACCCTAGAGACACTCAT

upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 5
------gtactggttttcactatgctgaattgtatccaatgtttaaatgttcaatgttctagctgacagtgacttgca---acagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT
       |  || ||| |  | |       | |  | || ||||   | ||   | | |   || |   | | ||  |   | |||| ||||| ||||| || || |||||||||| ||||||||| ||||| ||||||||||| || ||||| ||  ||||  |  ||
gttttctttgtgatttgctttctatcattgtttggcaaaagttttggt-ttttttttccatactaatgattatttatatttatagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATAGCAGCCATGAACCAAGCAATCCCCGAGATGCCAAT

upper sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 5
----------gtactggttttcactatgctgaattgtatccaatgtttaaatgttcaatgttctagctgacagtgacttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT
          ||| |   ||||||| |      |  | |   || ||| |    |  ||  |  |  |    |    |     ||||| ||||||||||| ||||| |||||||||| ||||||||| || |||||||||||||| || ||||| ||| | || || |||
gttaattttggtatttaatttcactctttaagttaatgttttatttttgatctattgatcctaaaatttggtgatcttaattccagGTTAAACTGATTGATTTCTCCCCTGGTGAGAAGTATTTGGTTACCTACAGCAGCCATGAACCAAGCAATCCTCGCGATACTCAT

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|31351129|gb|CD435486.1|CD435486
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
EST: gi|149098249|gb|EE184215.2|EE184215
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCCTTTTGCTCATTTCATG                         GGTGAA-CTGATTGAC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagG-TGAAACTGATTGAC
EST: gi|22542190|gb|BU092628.1|BU092628
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
EST: gi|32841675|gb|CD981356.1|CD981356
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
EST: gi|32841369|gb|CD981050.1|CD981050
EST:     GGGGCGGTGAAAATGGCTTCGCGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
EST: gi|60350764|gb|DN217737.1|DN217737
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
EST: gi|32841679|gb|CD981360.1|CD981360
EST:     GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATG                         GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC
genomic: GGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGC

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: 420

CCCTCTGGGAACCTACATGGCAACGGTTCATAGGCAGGGATCACAGGTGTGGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

CCCTCTGGGAACCTACATGGCAACGGTTCATAGGCAGGGATCACAGGTGTGGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

CCCTCTGGGAACCTACATGGCAACGGTTCATAGGCAGGGATCACAGGTGTGGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

CCCTCTGGGAACCTACATGGCAACGGTTCATAGGCAGGGATCACAGGTGTGGGGCGGTGAAAATGGCTTCGAGCGTTTGATGCGTTTTGCTCATTCCATGgtactggttt ... cttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtatccaatgtttaaatgttcaatgttctagctgacagtgacttgcaacagGTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT
                                 agctgac  putative branch site (score: 236)
          aatgtttaaatgtt  TA-rich tract