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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcataggctaattccatctcttagaaatgcaaactgtttagttttaattggctgtaggacaatgcattactcagttgcatttatggctgaatatttccctgttcttcaacgtctgcag

Basic information

species Zea mays
transcript GRMZM2G110233_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110233_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 7
---------TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcataggctaattccatctcttagaaatgcaaactgtttagttttaattggctgtaggacaatgcattactcagt-tgcatttatggctgaatatttccctgttcttcaacgtctgcag
         ||||||||||||||||| ||||||||||| |||||||||||||||||||| || ||||| ||||| |||||  ||  ||  |||| ||||||||||           | |||||| | |   |   |||||||| |||  || || |  |  |  || |     | |  | |   || | ||||                                       
TTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGTGATGAAAGCTGCGATAGACAGCATGGTTAATGATGCCACAAATGATGTTGATGgtaag-----------ttggctaacttcggttgccagaaatgctaac-attgagctacatgttactatcattta-taaactgtgcattgtgcag--------------------------------------
















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|60399828|gb|DN232638.1|DN232638
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAA
EST: gi|60348613|gb|DN215586.1|DN215586
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|4826173|gb|AI667801.1|AI667801
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|78025462|gb|DV493849.1|DV493849
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|12970246|gb|BG266887.1|BG266887
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAG-CCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|60401403|gb|DN234210.1|DN234210
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAA
EST: gi|15427127|gb|BI542949.1|BI542949
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|32936770|gb|CF041589.1|CF041589
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACAA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|13177895|gb|BG349078.1|BG349078
EST:     TGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|4314505|gb|AI461559.1|AI461559
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGA
EST: gi|18450820|gb|BM429098.1|BM429098
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAG
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAG
EST: gi|33092580|gb|CF052574.1|CF052574
EST:     TATTGACAGTAAGAAAAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
EST: gi|15079865|gb|BI388861.1|BI388861
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|60341811|gb|DN208784.1|DN208784
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
EST: gi|60356645|gb|DN223618.1|DN223618
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
EST: gi|18648777|gb|BM497596.1|BM497596
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTACGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCA-GAAAAAGAAGAC-A
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|4837466|gb|AI670556.1|AI670556
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|211350988|gb|FL171079.1|FL171079
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCA
EST: gi|60356892|gb|DN223865.1|DN223865
EST:     TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAG                         ATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC
genomic: TATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGC

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: 376

TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCAAAACCGAGACTGATGGTGATGCAATGGATGTGGATAAGCCCTCCAACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCAAAACCGAGACTGATGGTGATGCAATGGATGTGGATAAGCCCTCCAACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCAAAACCGAGACTGATGGTGATGCAATGGATGTGGATAAGCCCTCCAACGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 50

TATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGTGATGAAAGCTGCTATTGACAGTATGGTCAATGACACCTTAATGGATGATGATGGTAAGGCAGgtaagcatag ... acgtctgcagATAATGAGAAGGCGGACACATCTGCCAAGAAAAGCAAGAAAAAGAAGACCAAAACCGAGACTGATGGTGATGCAATGGATGTGGATAAGCCCTCCAACGT