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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagttttttattgtaatttaccagttacttttcaccatgtgacttgttcatgcttagtacttaggcatatttataagctatctttaagctttcatatcattatgtag

Basic information

species Zea mays
transcript AC203754.4_FGT008
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g38150.2 (Oryza sativa), 5'ss of exon 9
ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagttttttattgtaatttacca-gtt--acttttcaccatgtgacttgttcatgcttagtacttaggcatatttataagctatctttaagctttcatatcattatgtag
 |||||||  ||||| |||| ||||||||||| || || || ||||| || ||  || ||||||||||| | |||||||||||||| |||||| ||| || | | |||  ||   |||  | | ||  |||    || | | | | || ||||  ||    | | |      | |  |||                     
GTTGCTGATGATTTAGTTCTTGAGAAAACATCTTGCCCATTAGGTGTTCTCTTAATTGTTTTTGAGTCCCGACCTGATGCCTTGGTTCAGgtattttgttctggcaatgcactgtgttccattcttttccagaatacatatactt-ctaagtaactaattttgtgtc---attgttgttag--------------------

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 10
ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgt-agttttttattgtaatttaccagttacttttcaccatgtgacttgttcatgcttagtacttaggcatatttataagc-tatctttaagctttcatatcattatgtag
 | |  || ||  | || || ||||| |||||||||||||||||||||||  ||||||| ||||||||  | ||||||||| | || ||||| | |||   |||    |   |   ||  ||||  | |  | | |      ||||||| |    | || |  | | ||| |   |  ||  | ||   | | ||     
CTAGTAGATAAACTCATCCTGGAGAAGACATCATGTCCTTTGGGTGTCCTTCTGGTTATATTTGAGTCTCGACCTGATGCCCTTGTTCAGgttaatttaagattcctttcctcttatttgttttttcaacttcaataaac--tgcttagaa---ggacaaagatttgagcatgattacaaattatccatttagta-----

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G16510.1 (Glycine max), 5'ss of exon 7
ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagttttttattgtaatttaccagttacttttcaccatgtgactt--gttca--tgcttagtacttaggca-tatttataagctatc-tttaagctttcatatcattatgtag----------------------------------------------------
 | || || ||  | || || ||||||| |||||||||||||||||||||  ||||||| || |||||  | || |||||| | || |||||          | |   ||  |  ||    | ||   |    |||   || |  ||   || |  |  |||  | |    | ||||  |||    | |  |   | ||   |                                                     
CTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAGgttaagagaccctattccttctcgtttctaatccattctacatcttcaattaaaatgtcaaggatatgagcaacaatagagatctattattttgagtctagtgatactaatcaagttttgaaaatgtgtttattgtattaagatagttgttgaaattcattaatag

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G24530.1 (Glycine max), 5'ss of exon 11
ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagttttttattgtaatttaccagttacttttcaccat--gtgacttgttcat---gcttagtacttaggcatatttataagctatctttaagctttcatatcattatgtag
 | |  || ||  | || || ||||| | |||||||||||||||||||||  ||||||| ||||||||  | ||||||||| | || |||||   |||  |||   |||    |  |   ||||| | |   | |  || | |    |   |  | ||  ||||  ||| ||  | ||  |    | | |             
CTAGTAGATAAACTCATCCTGGAGAAGATATCATGTCCTTTGGGTGTCCTTCTGGTTATATTTGAGTCTCGACCTGATGCCCTTGTTCAGgttaatttaaattcccattccttatctgtctttcatcttcaataaactgcttagaaggacaaagatttgagcatgattacaaattgtccatttagtataa-------------

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: 132

ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagtttttt ... cattatgtagATTGCATCTTTAGCGATTCGAAGTGGCAATGGTCTTCTCTTGAAAGGTGGAAAAGAAGCCATGAGATCAAACAAAGTATTGCATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagtttttt ... cattatgtagATTGCATCTTTAGCGATTCGAAGTGGCAATGGTCTTCTCTTGAAAGGTGGAAAAGAAGCCATGAGATCAAACAAAGTATTGCATAAG


Block sizes: 31 (upstream exon), 47 (downstream exon)
Score: 21

ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagtttttt ... cattatgtagATTGCATCTTTAGCGATTCGAAGTGGCAATGGTCTTCTCTTGAAAGGTGGAAAAGAAGCCATGAGATCAAACAAAGTATTGCATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

ATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAGgtagtttttt ... cattatgtagATTGCATCTTTAGCGATTCGAAGTGGCAATGGTCTTCTCTTGAAAGGTGGAAAAGAAGCCATGAGATCAAACAAAGTATTGCATAAG