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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcacccataacatatcctacttctttatccctcctttgcatctgttcataactagcagcttgtactgtcataatatttggtacctctgttgattga...

Basic information

species Zea mays
transcript GRMZM2G078933_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078933_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g18180.1 (Oryza sativa), 5'ss of exon 3
CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcacccataacatatcctacttctttatccctcctttgcatctgttcataactagcagcttgtactgtca-taatatttggtacctctgttga--ttga-
||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| || || || |||||||| ||||||||| |||||  |  ||       | |   |  |  |||||||       ||| |||| |  |  || |||||  | || ||    || | |   | |   |||| 
CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcactaaacaccccaagaattatgtagttgctccttt----tgtttcttaaccaaaatattatactgctagtagtagcatgtgcttggatgggctttgag
















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|60354018|gb|DN220991.1|DN220991
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|23199554|gb|BU582119.1|BU582119
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|5268837|gb|AI770801.1|AI770801
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|211524509|gb|FK953544.1|FK953544
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGA
EST: gi|60349763|gb|DN216736.1|DN216736
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|22472860|gb|BU037340.1|BU037340
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|31349368|gb|CD433725.1|CD433725
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|29130800|gb|CB381504.1|CB381504
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|22935712|gb|BU571987.1|BU571987
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|31910180|gb|CD651295.1|CD651295
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAA
EST: gi|211270779|gb|FL137280.1|FL137280
EST:     CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGA                         ATTGCAAGAAGTTCAAGGACACTG
genomic: CGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 252

CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAAAGACCGAGGTGAAAGAAAACGAGGAAGTCTCCATTGCCGCCGCAGATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAAAGACCGAGGTGAAAGAAAACGAGGAAGTCTCCATTGCCGCCGCAGATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 296

CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAAAGACCGAGGTGAAAGAAAACGAGGAAGTCTCCATTGCCGCCGCAGATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcaccc ... tctatttcagATTGCAAGAAGTTCAAGGACACTGTTGAAGAGATAGCTGAAGAGCAAGGAAAGACCGAGGTGAAAGAAAACGAGGAAGTCTCCATTGCCGCCGCAGATTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcacccataacatatcctacttctttatccctcctttgcatctgttcataactagcagcttgtactgtcataatatttggtacctctgttgattga

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctcct