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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||||| || || |  |||  |||  | |||      |     ||  |  | ||||  ||||||||||  | |        | || ||  || |||||||||||||||||| ||  ||||||||||  | |||||||| |||||||| |||||||| |||||||||||||| || |||||||| |||||||||||
gtatgtttttgctgcttgtattttatgtttaa---gaaggcattcatgcagtagtaagatatggatttattt--------tgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttg-------ttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
                    || | | |||| ||||   | | ||  ||   |  || | ||  |    ||    ||  ||||| | |        || |||||||||||||||||| ||  |||| |||||  | ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||||| ||
-------------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
gtatggttatgatatttgcctttgctatttgtttcaagcatttttcttt---actagttggatatggattattctg-acaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
     || | | | | ||  |||  | || ||||  |  |||||  |     | |  | |  |||  |  ||  |  ||||  |  || | | |  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
-----gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
gtatggttatgatatt-tgcctttgctatttgtttcaagcatttttcttta---ctagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
     || | | | || ||  |||  | |||||||  |  |||||  |  |    |  | |  |||  |  ||  | ||||  |  || | | |  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
-----gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggt-acaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtatggttatgat-atttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||| |  |   || | |  | |||  | ||| |||   | |  ||   |   | ||   |||||| |   |  |        ||||| |||  ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || ||||| || |||||  | ||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattgg--------cttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
gtatggttatgat-atttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
|||||| |   || | |    |||  | ||| |||   | |  ||   |   | ||   || |||    |||     |     |||| |||  ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || |||||||| |||||  | ||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtgg----ttccattgat----ttttatgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
            ||  ||| ||    | |  || |       ||| |  | | |||       ||      ||  |    ||||   | |  ||||||||||||||||||  | || ||||||||  | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| |||||  | ||
-----------gtaagtgcgttatacagtgattgc-------tttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||| |    ||     ||    || ||  ||| |     |||||   |||| |  |  |||  ||||  | |        |||||  | |  |||||| |||||||||||  | || ||||||||| | | ||||||||||||||| || |||||||| || |||||||| || |||||||| |||||| | ||
gtaagtgcttgtgtactgaggctgttagatgtattgg--attttctcttac-atatatatactgatttcttt--------tctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
--gtatggttatgatatt-tgcctttgctatttgtttcaa-gcatttttctttactagttggatatggattattctgacaacattcttttttgtta-agCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
  |     ||     |||      ||||| |    |   |     |  |   ||  | | | |     |  ||| ||      || |    | ||  |||||| || || ||||| || |||||||||||  ||||||||||||||||||||||||| || ||||| |||||||| || ||||| ||||| ||| | ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

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|32929959|gb|CF034771.1|CF034771
EST:     AGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
EST: gi|33094019|gb|CF054013.1|CF054013
EST:     AGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG

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), 47 (downstream exon)
Score: 346

TTACAGTACACTATCGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

TTACAGTACACTATCGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 217

TTACAGTACACTATCGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 221

TTACAGTACACTATCGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTAGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggttat ... ttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
                             ttctgac  putative branch site (score: 221)
                                      cattcttttttgtt  putative PPT
                                       attcttttttgttaa  TA-rich tract