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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtagtctgtaacggggtgatctccggacaggcagcaattatagatttgcatgtttcctgtgtctaatcacacattcgaatggtcatccctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA

Basic information

species Zea mays
transcript GRMZM2G175867_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175867_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g08930.1 (Oryza sativa), 3'ss of exon 8
---acagtagtctgtaacggggtgatctccggacaggcagcaattatagatttgcatgtttcctgtgtctaatcacacattcgaatggtcatccctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA
   || ||   |  | |   |   || |       |||     || |   ||   | |    ||   |  | |  |  |||   ||  |      ||  |||||||||||||||||| |||| || ||||| || ||  ||||||| |||||||| |||||||| ||||||||||| |||||||| || || || ||||||||
tttaccgttcccattgatttgtaaatatgtaatttggcttgggttgtcatttgataagaagact---ttcacttgcgtattaacatattgtattatattgcagGGAAAGTTACAAGCCTTGTTGCGAAGAAAGATGTGACTTTAGCAACACGGATAGAAGAGGCTATGAAGAAAAACGAGAGCTTAGAGGCACTGACGACTAA
















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|67038766|gb|CO465021.1|CO465021
EST:     ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCCAAG                         GGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
genomic: ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
EST: gi|148986358|gb|EE030095.2|EE030095
EST:     ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG                         GGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
genomic: ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
EST: gi|33942668|gb|CF349268.1|CF349268
EST:     ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCCAAG                         GGAAAGTTACAAGCATTGTGGCTAAAAAGGACGTA
genomic: ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTA
EST: gi|6827364|gb|AW331007.1|AW331007
EST:     ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG                         GGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
genomic: ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
EST: gi|78123116|gb|DV541500.1|DV541500
EST:     ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAG                         GGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA
genomic: ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGA

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: 125

ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 27

ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

ATTGATTACCTTCACAGAACCGGGAGAACTGCACGCATGGGAGCCAAAGgtataagcaa ... cctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgcatgtttcctgtgtctaatcacacattcgaatggtcatccctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA
                                            ccctaac  putative branch site (score: 133)
                                        tcatccct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtagtctgtaacggggtgatctccggacaggcagcaattatagatttgcatgtttcctgtgtctaatcacacattcgaatggtcatccctaacgcagGGAAAGTTACAAGCATTGTGGCTAAGAAGGACGTAGCTTTAGCTACACGGATTGAAGAGGCCATGAAGAAAAATGAGAGCTTGGAAGCTCTCACGACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - -gcagcaa
- - - - - - - - - - - - - - - - - - - - - - - atttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacattc