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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtttatttgccagagtactctgcagctaacttcaatacccagcataaatccgtattacgttgcaccttgattaatgtgccttgtgatggtttcatccag

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 8
TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagttt-atttgccag----agtactctgcagctaacttcaatacccagc-------------ataaatccgt--attacgtt--gcaccttga---ttaatgtgccttgtgatggtttcatccag
|||| || ||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||| || |||||| |||||| |||| ||||    || |||||||     | |  ||||||   |              | | |  ||  |||||  |  || |||| |   |||    | ||||| ||| ||   |||||
TGTTAGACATTGAATGCTTCTCTTATCTTAATCGTGCTTTGGAGAGCCCATTATCACCAATTGTGATACTTGCTACGAACAGAGGAATATGTAACGTAAGgtaaacagtttgatttaccagtcgaagcactctgcgctacattataataccagactaatcatgtgtttgtcagtttgtttattaccatatgctccttaaagtttacaaagtcttgttatgcttgtgtccag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 8
TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagttt-atttgcca----gagtactctgcagctaacttcaatacccagcataaatccgtattacgttgcaccttgattaatgtgccttgtgatggtttcatccag---------------------------
|| | |||||||||||||| ||||||||||| |||||  ||||||||||||||||||||||||||||||| || || |||||||||||||||||||| |||||| | |||| |||| ||      || ||||||   |  | | || |||| ||  |||  | |  |      |    |  |||| | |||    | | | |  ||                                
TGCTAGATATTGAATGCTTCTCTTATCTTAATCGTGCTCTGGAGAGCCCATTATCACCAATTGTGATACTTGCGACAAATAGAGGAATATGTAATGTAAGgtaaacggtttgatttaccgctcgaagcactctgtcac--attgcagtacc-agagtaatactgcgtctatcagtttgtctattactatgctccttaaagttaacaagtcttttatatacttgtgtgaatgtgtccag
















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|32932061|gb|CF036873.1|CF036873
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACTGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|60342617|gb|DN209590.1|DN209590
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|74241474|gb|DT649388.1|DT649388
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|4826086|gb|AI667714.1|AI667714
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|32842037|gb|CD981718.1|CD981718
EST:     TTATCGCCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACTGATATGCCGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|21331671|gb|BQ487052.1|BQ487052
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|22819003|gb|BU499093.1|BU499093
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTCATGTGAG                         AGGAACCGATATGACGAGTCCACATGGGATACCAGGGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|32840485|gb|CD980166.1|CD980166
EST:     TTATCGCCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACTGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|67016264|gb|CO445013.1|CO445013
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|78103432|gb|DV521860.1|DV521860
EST:     TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAG
EST: gi|32842224|gb|CD981905.1|CD981905
EST:     TTATCGCCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAG                         AGGAACTGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
EST: gi|71420713|gb|DR805175.1|DR805175
EST:     TAGAGGAATATGTAATGTGAG                         AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG
genomic: TAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAG

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), 49 (downstream exon)
Score: 159

TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 83

TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 73

TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 68

TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtt ... tttcatccagAGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTAATGTGAGgtaagcagtttatttgccagagtactctgcagctaacttcaatacccagcataaatccgtattacgttgcaccttgattaatgtgccttgtgatggtttcatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA