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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatatttcagtatttgtattctttgacgattttaaatcatactaactgctaaggtgtcaatcacgctaagtttacatgatcaataatcataacta...

Basic information

species Zea mays
transcript GRMZM2G305007_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305007_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 5'ss of exon 15
GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatatttcagtatttgtattctttgacgattttaaatcatactaactgctaaggtgtcaatcacgctaagtttacatgatcaataatcataacta---------
 || |||||  |||| |||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||||||||  ||       |   |||  ||| |  | | ||| ||||| ||  | |      | ||| | ||      |||||| ||  | |||  |  ||||            
CTACAAAGTCTTGGGCAGTTCATACCCATGGATTGCAAGAAAAGTTCTCACAGACAGCTCACCAAAGCTCCGATCAACTTTGCAGACGCTTCTTTATAAGgtcaat------taaccttttaattttcaggcaattataaattatgatgaaac---aagtgaccatgctagcaagtttgcaaaaccaaagaagataataggaatacagg

upper sequence: GRMZM2G305007_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv18s0001g01620.t01 (Vitis vinifera), 5'ss of exon 15
GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatatttcagtatttgtattctttgacgattttaaatcatactaactgctaaggtgtcaatca---cgctaagtttacatgatcaataatcataacta-----------------------------------
 || |||||| | || ||| |||| ||||||||||| ||||||||||| |||||||| ||||| || ||    ||  |||||||| ||||||||||||||||  || |||   |   ||| | ||| || | |  | | | |  | |   |||   | || | || |     | |   | ||||  | ||||  | |||   |                                   
TTACAAAGTTTTAGGTAGTACATACCCATGGATTGCTAGAAAAGTTCTAACTGACAGCTCACCCAAACTGAAGTCTTCTTTGCAGGCTCTTCTTTATAAGgtaaatctatgaaaac-tttcttttccttcaagtatgtcagttttgcc--ctgtacatgtattaacctgattgttctctctacacaaacaatgtttatatagaaccactatccctgattctagaatgtgtcttgttag

upper sequence: GRMZM2G305007_T03 (Zea mays), 5'ss of exon 9
lower sequence: PP1S199_8V6.1 (Physcomitrella patens), 5'ss of exon 15
GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatatttcagtatttgtattctttgacgattttaaatcat---actaactgctaaggtgtcaatcacgctaagtttacatgatcaata-atcataacta
 |||||||| ||| | ||||||||||||||||| ||  | || || ||||||||||  |||||||||||||| || ||| | |||    |  | || || ||  |  |  | ||       |  |||      |||||||            | |    ||   |   |     |  || ||  |  |   |  || ||| |  
CTATAAAGTACTGAGTAGTTCATATCCATGGATAGCGCGGAAGGTCCTCACTGACAAATCACCAAAGCTTCGGTCCACTCTTCAGGAAATAGTATACAAAgt--acttgctacatatcccttcctctcgtgtaattttaagctgatgggtcgattctcgagtctttttttgttttttgtataagttttgcttgtattatacc--

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|6020457|gb|AW065385.1|AW065385
EST:     CTGACAGTTCGCCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAG                         GATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG
genomic: CTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG
EST: gi|6194572|gb|AW146676.1|AW146676
EST:     CTGACAGTTCGCCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAG                         GATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG
genomic: CTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG
EST: gi|71768064|gb|DR966001.1|DR966001
EST:     GATCAACTTTGCAGACTCTTCTTTATAAG                         GATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG
genomic: GATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG

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: 47 (upstream exon), 38 (downstream exon)
Score: 23

GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 20

GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 4

GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 5

GTATAAAGTTCTGGGGAGTTCATATCCATGGATTGCAAGAAAAGTTCTCACTGACAGTTCACCAAAGCTTCGATCAACTTTGCAGACTCTTCTTTATAAGgttgatatat ... tatgttacagGATGGCACTTTCCAAATTGATCGCCTGGAATCTTTGTTAACTGAG