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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC

Basic information

species Zea mays
transcript GRMZM2G470438_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC--------------------------------
            |  | | || |  |    || | |||| | |    ||  || |||  |    |  ||  |||||||||| ||         ||||   | | | |             |||||   ||          ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||                                
------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgta----tattgagttgtgccactaaa---------atatt--tgactga-------------ttgactcctttc------gcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA

upper sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0044g01570.t01 (Vitis vinifera), 3'ss of exon 5
gtaa--aaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttcc-agGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC--------------------------------
||||  || | |   | | |      |  ||    ||  |||| | | |  |||  |||   |   |      |||    |||  |  ||| ||| | | || |  || |||     |  |||     | || |  || | ||||  |||| || ||||| || |||||||| ||||||||||||||||||||| |||| || || | |||||||||                                
gtaatgaagattaagtatctgtttttagcttaaggttggttattgaattgtctttttat---ggtctataattttgaattact--agtcatttactttttcagacattgaaagtgaact-attccttttcttttacttgtctttcttagGCTGGCATTGGTACAGATGCAACAATGCATGATCACATAAAAAAGCTGCTGGATCGGTTTTATGCAACTAAGGACTCAAATACTCGTTTCTCACCAACAA

upper sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 4
lower sequence: EFJ13984 (Selaginella moellendorffii), 3'ss of exon 12
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaa-atcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC--------------------------------
                                                                                                | | || ||  |  ||  |  |||  ||| ||| |||     |    |||||  |||||||| || ||||| || ||||||||||||||||||||| |||| |||||  | || || ||                                
-------------------------------------------------------------------------------------------gtggtttcttagttccagcattttcaagacctga-attctct----gtgcggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA

upper sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28114 (Selaginella moellendorffii), 3'ss of exon 12
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaa-atcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC--------------------------------
                                                                                                | | || ||  |  ||  |  |||  ||| ||| |||     | |  |||||  |||||||| || ||||| || ||||||||||||||||||||| |||| |||||  | || || ||                                
-------------------------------------------------------------------------------------------gtggtttcttagttccagcattttcaagacctga-attctct----gtgtggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA

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|148978925|gb|EE026381.2|EE026381
EST:     GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAA                         GCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT
genomic: GGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... atatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTT




















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), 45 (downstream exon)
Score: 43

TTTGTTCCGACAACTTTAACACTTGATTCTGGAGTGACTCGGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... atatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC


Block sizes: 43 (upstream exon), 30 (downstream exon)
Score: 6

TTTGTTCCGACAACTTTAACACTTGATTCTGGAGTGACTCGGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... atatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC


Block sizes: 41 (upstream exon), 33 (downstream exon)
Score: 3

TTTGTTCCGACAACTTTAACACTTGATTCTGGAGTGACTCGGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... atatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 7

TTTGTTCCGACAACTTTAACACTTGATTCTGGAGTGACTCGGCCACCGCCTCTTCTGGCTGAAGCCGACCTTCTTAGCTGTATGGATAAAgtaaaaaaat ... atatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatccataatttaaaatcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC
                           atttgac  putative branch site (score: 7)
                                              tatttcc  putative PPT
                           atttgacattttctta  TA-rich tract