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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgcaatcgcacctcagtcttttgcgatatgtgtttttatgcagaaactttaacctgcgtgctgatacaagtaagatataactcattctcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG

Basic information

species Zea mays
transcript GRMZM2G336858_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G336858_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g28980.1 (Oryza sativa), 3'ss of exon 10
--acatgcaatcgcacctcagtcttttgcgatatgtgtttttatgcagaaactttaacctgcgtgctgatacaagtaagatataactcattctcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG
    |    ||   |   ||  |       | ||||   ||    |   ||| |||   |   |    ||| ||  ||| |    ||   ||  ||   ||||||||||||||||||||||| |||||| |||||||||||||||||| | || || | |||  | ||||| || |||||||||||||| ||| | ||||||
tattacatgatgcaattccatgcagaaatcacatgttccttacatcgataacattatgttatttatgcataaaa--aagtttgcgctggatcattttcccagGGATGTGAAGATGGGGTACAGGAGGCTGAAGGAGAAGGTCAAGGAGCAGAAGAGGAAGGAAACGAAATTGTACGGCAACATGATTTCGAAGCTAAGCAAG
















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|5714360|gb|AI944345.1|AI944345
EST:     TGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGCCANCAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|211411217|gb|FL076934.1|FL076934
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|211411218|gb|FL076935.1|FL076935
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|60343806|gb|DN210779.1|DN210779
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|67022530|gb|CO451279.1|CO451279
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|211411221|gb|FL076938.1|FL076938
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|211411222|gb|FL076939.1|FL076939
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|60350756|gb|DN217729.1|DN217729
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|149060210|gb|EE157184.2|EE157184
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGCCACCAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|211411220|gb|FL076937.1|FL076937
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|5791270|gb|AI978062.1|AI978062
EST:     TGGCA-AGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|18383581|gb|BM416781.1|BM416781
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|60400590|gb|DN233397.1|DN233397
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|110541157|gb|EE045077.1|EE045077
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAA
EST: gi|14191396|gb|BG833626.1|BG833626
EST:     TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAG                         GGATGTGAAGATGGGGTACA
genomic: TTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACA

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: 121

AGGCCTTGTACAGAAGGGCACAGGCACACATGCATCTTGTTGATCTTGATTTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

AGGCCTTGTACAGAAGGGCACAGGCACACATGCATCTTGTTGATCTTGATTTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

AGGCCTTGTACAGAAGGGCACAGGCACACATGCATCTTGTTGATCTTGATTTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

AGGCCTTGTACAGAAGGGCACAGGCACACATGCATCTTGTTGATCTTGATTTGGCAGAGGCAGATATCAAGAAAGCTCTAGAAATAGATCCTGACAACAGgtaatgcttt ... tcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaactttaacctgcgtgctgatacaagtaagatataactcattctcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG
                                atataac  putative branch site (score: 101)
                                      ctcattctcttcatc  CT-rich tract
                            taagatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgcaatcgcacctcagtcttttgcgatatgtgtttttatgcagaaactttaacctgcgtgctgatacaagtaagatataactcattctcttcatcagGGATGTGAAGATGGGGTACAAGAGGCTAAAGGAGAAGGTCAAGGAGTACAAAAGAAGGGATGCCAAATTATATGGCAACATGATTTCCAAGTTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
acatgca
- - - - - gcacctc
- - - - - - - - - - cttttgc
- - - - - - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgtgc