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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaagctgctcatcttgtgacaaacttctgttaccctccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA

Basic information

species Zea mays
transcript AC217947.4_FGT002
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 15
gtaatcaagctgctcatc-ttgtgacaaacttctgttaccctccaa-cccgta-----acccagtg--gctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
|||||  | || ||   | || | | | |  | ||||   || |||   | |         ||| |  ||||| | ||| | ||||||||  |  |||||| || ||||||||||||||||||||||| |||| |||||| || ||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||
gtaattgaactacttgacattttcatacatgtttgttgatctgcaaattcatgtttttgttcagcgttgctcatatttcctacctttgtctgt--ccagGCTTCCGAAATCTGGGACATGATCTCCCAGGGTGGTTACATTTACGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCA

upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA17G07050.2 (Glycine max), 3'ss of exon 16
gtaatcaagctgctcatcttgtgacaaacttctgttaccctccaacccgtaacccagtggctcacagttcttgcc--tttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
          | || ||  |  || | | || | |||     ||| |  |  |    || || |   |  |   |  ||  |     | ||||| || ||||| |||  |||||| || ||||| |||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | |  || || || |
---------gtacttattctcggatacaatt-tattaattatcaatcaatg-cggtatgccttatcttaatcaacggttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAA

upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
gtaatcaagctgctcatcttgtgacaaacttctgttaccctccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
||| | |  ||  |   |   |   |    | | |||||   |||| ||  |  |  || ||   | ||   |  ||  |     | ||||| || ||||| |||  |||||| || ||||| |||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | |  || || || |
gtactta--ctttttcccagatacgatttatttattaccaatcaacgcggtatgccatgcctt--aattgacgg-ttcatgtgcctgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA

upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaatcaagctgctcatcttgtgacaaacttctgttaccc-tccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
       |   ||| ||       ||||  || | |   | |  |      ||  |||   ||     |      |||| | || | | |||| ||||| |||||| | |||||||| ||||| |||||  | ||||| ||||||||||||||||||||||| ||||| || || |||  |||||| || |
-----gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgc-agGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA

upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 16
------------------------------gtaatc--aagctgctcatcttgtgacaaacttctgt-taccctccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
                               | |||  ||| |  |  | |||  | | |  | | | |    |     || |      | |   |  ||| | ||  ||  |  || || |||| || || || ||| |  | || || || || |  ||||| |||||||||||||| |||||||||||||| || || || || |||  ||| |||||||
gtacgggactctcatttctcagaagggccattcatctgaagtttttgtttttgatatatatatatatatgtattattgtccatttgtttgagatgctaagtgcatgt-ttgctttatatctagGCGTCGGATATTTGGAATGTAATTTCTCAGGGAGGCTACATTTATGTCTGTGGTGATGCCAAAGGCATGGCAAGGGATGTCCACAGAACTCTTCATACCA

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|92087911|gb|EB484142.1|EB484142
EST:     CGCGCCAGGGCCTCGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAA                         GCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT
genomic: CGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT
EST: gi|32842091|gb|CD981772.1|CD981772
EST:     CGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAA                         GCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT
genomic: CGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT
EST: gi|32842090|gb|CD981771.1|CD981771
EST:     CGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAA                         GCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT
genomic: CGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGT

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: 46 (upstream exon), 44 (downstream exon)
Score: 44

GAACAATTTCGTTGAGCAAGGAGCACTGTCTGAGCTGGTTCTTGCCTTCTCGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 369

GAACAATTTCGTTGAGCAAGGAGCACTGTCTGAGCTGGTTCTTGCCTTCTCGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 387

GAACAATTTCGTTGAGCAAGGAGCACTGTCTGAGCTGGTTCTTGCCTTCTCGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

GAACAATTTCGTTGAGCAAGGAGCACTGTCTGAGCTGGTTCTTGCCTTCTCGCGCCAGGGCCTTGCTAAGGAATATGTGCAGCACAAAATGGCACAGAAAgtaatcaagc ... ccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccctccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA
                       ggctcac  putative branch site (score: 315)
                                ttcttgcctttgtcca  putative PPT