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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggtctaccatagttacataggtcattactagtcatgaggtatattggtttcaggcatcaggtctagctatgtctgtttacaacattgatttgttataaatacgttacctttttgacatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG

Basic information

species Zea mays
transcript GRMZM2G330772_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330772_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 9
gtatgtggtctaccatagttacataggtcattactagtcatgaggtatattggtttcaggcatcaggtctagctatgtctgtttacaacattgatttgttataaatacgttacctttttgacatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG
||||||  || |  |||  | |||   |  || ||    ||| | ||      |||  || | ||  |  |  | ||    | | |    || |   ||  ||||  |   ||| | ||    ||| |||||||| ||||||||||| || |||||||| || || ||||||||||| ||||||||||||||||||||||||||||| |||
gtatgttatccaatata--tgcat---ttctttctg--tatgggataatgcctttttggggaccaactacatttttgcggttctgcc-tgttcaca-gtactaaaatctcaaccatatttgtctttccagATACTGGACACTGTTGCAGAGATACAGGAACGTCACGATGCTGTAAGAGATCTAGAGAGGAAGCTTCTGGAGTTGCAGCAG

upper sequence: GRMZM2G330772_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtggtctaccatagttacataggtcattactagtcatgaggtatattggtttcaggcatcaggtctagctatgtctgtttacaacattgatttgt--tataaatacgttacctttttgacatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG
                  | || ||  ||  |  || | |||     | ||  ||| |    |    |   |   |||  |||   |   |||||||||  | |  | || ||  ||           ||||||| | |||||  | |||||||| || |||||||||||||| || || ||  |||||||||||||||| ||  | || |||
-----------------atcacttaactc--tcataattatgt--cttcttaattttatttttgtttttgcgagttgttggttgggagttttgatttgtattgtggacacattggct-----------gcagATAATGGACACATTGGCTGAAATTCAAGAGCGACATGATGCAGTTAGAGAAGTAGAGAGGAAGCTTCTTGATCTACAGCAG
















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|211226397|gb|FL202746.1|FL202746
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGARGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211421982|gb|FL437726.1|FL437726
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211224343|gb|FL202744.1|FL202744
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGARGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211202912|gb|FL437151.1|FL437151
EST:     CAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: CAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211495566|gb|FL127190.1|FL127190
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211226398|gb|FL202747.1|FL202747
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGARGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|60359751|gb|DN226724.1|DN226724
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|211224342|gb|FL202743.1|FL202743
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|67020224|gb|CO448973.1|CO448973
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGACAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|60395077|gb|DN227946.1|DN227946
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|67020710|gb|CO449459.1|CO449459
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
EST: gi|9732911|gb|BE511663.1|BE511663
EST:     AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAG                         ATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT
genomic: AAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGAT

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), 48 (downstream exon)
Score: 177

ACAATTGATGACTTGATAGAGACCGGAAAAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

ACAATTGATGACTTGATAGAGACCGGAAAAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

ACAATTGATGACTTGATAGAGACCGGAAAAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

ACAATTGATGACTTGATAGAGACCGGAAAAAGTGAGCAAATATTCAAAGATGCTATCCAACATCAGGGAAGAGGCCAGgtatgtggtc ... acatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgtttacaacattgatttgttataaatacgttacctttttgacatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG
                                        ttttgac  putative branch site (score: 151)
           aacattgatttgttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggtctaccatagttacataggtcattactagtcatgaggtatattggtttcaggcatcaggtctagctatgtctgtttacaacattgatttgttataaatacgttacctttttgacatttgcagATACTAGACACTGTTGCTGAAATACAGGAGCGACATGATGCTGTAAGGGATCTAGAGAGGAAGCTTCTGGAGTTGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA