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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatttcacacgactggtttaatcagtggcagacgccacttctgtatttattcagtttgctttttaatgtgtattcttgggaaaattatcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 2
-----gtacaatttcacacgactggtttaatcagtggcagacgccacttctgtatttat-tcagtttgctttttaatgtgtattcttgggaaaattatcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG
      |  |||| |  || ||   |  |||   |   |||    | ||   || | || |   | | |  | ||   | | | |     |||||    |   |||||||||||||| ||| | |||   |||||||| | ||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||  ||||||
gctatttttaattgcttactaccattaaaat--attttagaacatatttagctaatgatatttttctaccatgtaccttttctccccccaaaaat----attgcagACATCTGATGATGCAATTCCACAGCCAGTTGTTCTGATAGATCAAGACTCAGACCGTGATGCAACCATAGTGCAGCTGAGTTTTGGAGACCGTCTGGGGG
















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|31351917|gb|CD436274.1|CD436274
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|26558566|gb|CA830801.1|CA830801
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|211033888|gb|FL356298.1|FL356298
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATARMATCAGGACTC
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAG-ATCAGGACTC
EST: gi|8368912|gb|BE051857.1|BE051857
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|211241644|gb|FL328623.1|FL328623
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGAWAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|87157787|gb|DY402576.1|DY402576
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     TTTG-TGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGCTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|22545865|gb|BU098239.1|BU098239
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|6526657|gb|AW215948.1|AW215948
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA
EST: gi|211502811|gb|FL321803.1|FL321803
EST:     TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAACG                         ACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCH
genomic: TTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCA

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: 230

AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 615

AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACGgtacaatttc ... atcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatttattcagtttgctttttaatgtgtattcttgggaaaattatcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG
                   ttttaat  putative branch site (score: 279)
                                              tcacccc  putative PPT
                  tttttaatgtgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatttcacacgactggtttaatcagtggcagacgccacttctgtatttattcagtttgctttttaatgtgtattcttgggaaaattatcaccccagACATCTGATGAGGCAGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC