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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcttttcttcttattttaacatgctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 23
gtcatcttttc--ttcttattttaacatgctac--gatagttgcca------ggtcat---gttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||  | |  ||  |||| | ||||| ||| | |  ||||  |||||      | | ||   |||  ||| |||| || || ||||||||| ||||||||  |||||||||| |||||||| ||||| ||| | |||||| ||||||||||||||||||| ||||||
gttctttgctcatttctcaatttaa-atgttgcttgataaatgccaatgcttgattatattgttactgagataaaccttcctgcagATATCAAAGGCTTCCTAAGTGATGTCAAACCAGCGCTTCTCAGTACTCTGGATGCTGAATATGAGAAAAATCCATTTGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 23
gtcatcttttcttc-ttattttaacatg--ctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||||  ||   ||   |||   |   ||   |     | ||      ||| |    | |  |  | |  |||||||| |||||||| ||| | | |||||| ||||| ||||| || |||||||||||||| || |||||||| ||||| ||||||
gtcactttgcgttaactatcaaattttgatttctctcaatttgtttttcaaggctctaaggtttttctccttgcagACATTAAAGGGTTTCTTACTGATGTAAAACCTGCACTGCTCAGTGCCCTGGATACGGAGTATGAGAAGAATCCATTTGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 25
gtcatcttttcttcttattttaacatg---ctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
||||  ||   ||    ||  ||  |     |     | ||      ||| |    | |  |  | |  |||||||| |||||||| ||| | | |||||| || || ||||| || |||||||||||||| || |||||||| ||||| ||    
gtcactttgcgttaactttcaaattttgatttctctcaattttgttttcaagGCTCTAAGGTTTTTCTCCTTGCAGACATTAAAGGGTTTCTTACTGATGTAAAGCCTGCACTGCTCAGTGCCCTGGATACAGAGTATGAGAAGAATCCATT----

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 23
-----------------------gtcatcttttcttcttattttaacatgctacgatag-ttgccaggtcatgttcttgaaataatccatct-----tgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
                       |       ||  ||| | ||     || ||  |||  ||  |    ||     |  || | ||   | |     | |||| |||||||| ||| | | |||||| ||||| ||||| |||||||| || || || |||||||||||||| ||||| |||
gtggctacgaattcctttaagctggttcagctttgtctaaattctgtttggtagaataacttatcttaacactgaatcaaacttatgtttttctgttttcagACATTAAAGGGTTTCTTAATGATGTCAAACCTGCACTACTAAGTGCACTTGACACCGAATATGAGAAAAACCCTTTCGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 22
gtcatcttttcttcttattttaacatgctacgatagttgccagg-tcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
               | ||| |       | | |   |   | | | | ||| || |  |      | || |||   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | ||||
--------------gtttttcagataatgatgttgaatataaagcttacgtttttaagttc-----tgtttcagGCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ15655 (Selaginella moellendorffii), 3'ss of exon 22
gtcatcttttcttcttattttaacatgctacgatagttgccagg-tcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
              || ||   |||    | | |   |   | | | | ||| || |  |      | || |||   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | ||||
-------------gtttttcagaca-atgatgttgaatataaagcttacgtttttaagttc-----tgtttcagGCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAG

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|19350672|gb|BM895204.1|BM895204
EST:     AAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAG                         ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGG
genomic: AAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGG




















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: 368

ATTGATTTTTGCAAAGACATCGGTCTTCAGTCTAGTGCTGCTGTAACAAGAAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 109

ATTGATTTTTGCAAAGACATCGGTCTTCAGTCTAGTGCTGCTGTAACAAGAAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

ATTGATTTTTGCAAAGACATCGGTCTTCAGTCTAGTGCTGCTGTAACAAGAAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

ATTGATTTTTGCAAAGACATCGGTCTTCAGTCTAGTGCTGCTGTAACAAGAAATGCTACTATAAAACTAATTGGGATGCTACATAAGTTTGTGGGCCCAGgtcatctttt ... catcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaacatgctacgatagttgccaggtcatgttcttgaaataatccatcttgcagATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG
 ttttaac  putative branch site (score: 270)
                                           tccatctt  putative PPT
                                  ttgaaataat  TA-rich tract