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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT

Basic information

species Zea mays
transcript GRMZM2G039396_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 3
gtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT
||| |||||| ||||||  |||| |||||         || |           || |  ||||   ||||||||      | || |     || |||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||| ||| || |||| || ||||||||||| |||||||||||||||||
gtgtttattgtagtgtgcaattgctgttt---------tgtt-----------tttgatgattcagataagaatacggtgatttcggtg--cttagGTGTGTATGCTGGTGATCCTTCAAAGCTCAGTATGAAGGCTGCATTTGGGAAGGTGTGGAGGCTGGAGGATACTGGAGGTAGCATTATTGGTGGAACCAT

upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------gtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT
                                 ||||| || |  | | |    |  | |  |   ||   | ||       ||   | | | |      |||     |  |||       | |||||| ||||||||||||||||| || || |||||||| || || |||||||||||||||    | ||  ||| ||| || || || || ||||| ||  |
gtagagttatagataaaacttcatgtgaaccatttatt-catttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
















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|149005349|gb|EE039900.2|EE039900
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAANGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
EST: gi|149071120|gb|EE159520.2|EE159520
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
EST: gi|78079002|gb|DV507414.1|DV507414
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
EST: gi|211265727|gb|FL016769.1|FL016769
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCNTCTA-GCTCAGCATGAAGGCTGCATTT
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTT
EST: gi|211265725|gb|FL016767.1|FL016767
EST:     CAACCTCGGTGCTGAAGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGG
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGG
EST: gi|78087541|gb|DV515934.1|DV515934
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGA
EST: gi|211265728|gb|FL016770.1|FL016770
EST:     CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG                         GTGTCTATGCTGGTGATCCNTCTA-GCTCAGCATGAAG-CTGC
genomic: CAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGC

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: 77

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAGgtgcttattg ... taaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT
                               atttaac  putative branch site (score: 86)
                         ataagaatttaacaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA