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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctaaccgggacgtgctttgttctgtgttctttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

Basic information

species Zea mays
transcript GRMZM2G076337_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076337_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
---gttctaaccgg---gacgtgctttgttctg--tgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA
   |||||     |   |  |  |||||   |   ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| |  | | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA

upper sequence: GRMZM2G076337_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 3
----------------------------------------gttctaaccgg---gacgtgctttgttctgtgt-----tctttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA
                                        |||||     |   |  |  |||||   |   |     |  |||||  || ||   | ||||| |      || |    |  ||| ||| |  |||||| ||  |||||||| |||| ||| |  | | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
gttgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgttatgcttaatatatta------atatagactggtgaacttcgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA

upper sequence: GRMZM2G076337_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 3
gttc-taaccgggacgtgctttgttctgtgttctttgttctttgtgtacactatatcaccaaccatgttccttcctgatc-tttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA
|||  ||      || |  | |  | || |  |||||   |   | || | | |   |  |   ||| |   | |   |  |||   ||||  || ||||| ||  | || ||| |  |||||||||| ||| |||||||||||| |||||  ||||| ||||||||||| ||||| || |    |||||
gttagtatttaaaacttcttctagtttgcgacctttgaaatcaatataga-tgtgagagtatatatgctaactaccatttgttttttcagAGTTTTTCATCGCCGTTAAACCAGGTGCAGAACAGGATTTGGTTGATGCATTGGGGTCTGTATATCTTTTTTAACCATGATAATGGAAGGACACAGATCA

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|5713763|gb|AI943755.1|AI943755
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaaccg ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCAT




















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: 27 (upstream exon), 49 (downstream exon)
Score: 215

GAGTGCCGTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaaccg ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 173

GAGTGCCGTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaaccg ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 186

GAGTGCCGTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaaccg ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 155

GAGTGCCGTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaaccg ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgggcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA
                                      tcctgat  putative branch site (score: 155)
                                 ttccttcctgatcttt  CT-rich tract
               actatat  TA-rich tract