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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatctgtcttagaaatactaagtcaaatgttccgcattagcttgcaacccaaagtcttccgcagatagtaatgatatacggaatatcacatttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC

Basic information

species Zea mays
transcript GRMZM2G394827_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G394827_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g46430.2 (Oryza sativa), 3'ss of exon 1
tctatctgtcttagaaatactaagtcaaatgttccgcattagc--ttgcaacccaaagtc---ttccgcagatagtaatgatatacggaatatcacatttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC------------------
                       | |||||||| ||   ||    |   |       |||   ||   | | |  | || |  ||| | || | ||| | ||  |||| | ||| |||| ||||||||| |||||||| || ||||| | |  | |||||||| || |||| | ||||||||||| |||||| ||||||||||||                  
-----------------------ggcaaatgttgcgttataataatcatatatatgggtcactttttcctgctgatcattagttacaggatcttacagtaggttgttggttttggttatgtagGCGAAGCGAAATGGCGACGGTTCCGGAGCCTTTGATCTGGGAGATTGTCAAGAAGAACAACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAG

upper sequence: GRMZM2G394827_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57540.1 (Oryza sativa), 3'ss of exon 1
tctatctgtcttagaaatactaagtcaaatgttccgcattagctt-gcaacccaa-agtcttccgcagatagtaatgatatacggaatatcacatttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC------------------
                    |    | |  |||  | | |   || ||     ||  |||       | |   |  |  ||  |  ||     | | | |  |   | ||| | || |||    || |||||||| || ||||| | |  | || ||||| || |||||| ||||||||||| |||||| |||||||||||                   
-------------------ttgctgccagcgttgtgtaatgtttttgcgtgttaatggtcacttagtggtctgatggtcatttgctatggtgtaatggtcgatctgt-ttggtgatgtagCTACAGCGAAATGGCGACGGTTCCGGAGCCTTTGTTCTGGGAGATTGTGAAGAAGAACAACTGCTTCCTCGTGAAGCAGTTTGGAAACAGCAATGCCAAG
















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|211374744|gb|FL076482.1|FL076482
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|33095001|gb|CF054995.1|CF054995
EST:     CACCCCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|89755970|gb|DY686188.1|DY686188
EST:     CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374751|gb|FL076489.1|FL076489
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACG-CGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGTAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|33092136|gb|CF052130.1|CF052130
EST:     CACCCCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374742|gb|FL076480.1|FL076480
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|9824966|gb|BE575063.1|BE575063
EST:     CAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|60343518|gb|DN210491.1|DN210491
EST:     CAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|9732890|gb|BE511642.1|BE511642
EST:     GCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: GCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374743|gb|FL076481.1|FL076481
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|60347212|gb|DN214185.1|DN214185
EST:     AGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: AGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374749|gb|FL076487.1|FL076487
EST:     CAGAGCGAGGCGACG-CGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|60395199|gb|DN228068.1|DN228068
EST:     CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|71596060|gb|DR906811.1|DR906811
EST:     CCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211372087|gb|FL076475.1|FL076475
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACG-CGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211372088|gb|FL076476.1|FL076476
EST:     ACCTCAACCCAGGAACAGAGCGAGGCGACG-CGSGGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: ACCTCAACCCAGGAACAGAGCGAGGCGACGCCG-CGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374747|gb|FL076485.1|FL076485
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|89246801|gb|DY618588.1|DY618588
EST:     CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211372089|gb|FL076477.1|FL076477
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCA-CTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374752|gb|FL076490.1|FL076490
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACG-CGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGTAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211374741|gb|FL076479.1|FL076479
EST:     CACCTCAACCCATGAACAGAGCGAGGCGACG-CGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|211372086|gb|FL076474.1|FL076474
EST:     CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|60347198|gb|DN214171.1|DN214171
EST:     GACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: GACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|37418286|gb|CF646811.1|CF646811
EST:     CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|33091021|gb|CF051015.1|CF051015
EST:     CACCCCAACCCAGGAACAGAGCGAGGCGACNCCNCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|60398464|gb|DN231280.1|DN231280
EST:     CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: CAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
EST: gi|33467201|gb|CF244250.1|CF244250
EST:     ACCTCTTCTCCG                         TTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT
genomic: ACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCT

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: 1107

CCTGGTATAAAAGAGGCGAGGGTCACTGATGCAGGACCTCCCGCAGCCGCCACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 954

CCTGGTATAAAAGAGGCGAGGGTCACTGATGCAGGACCTCCCGCAGCCGCCACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 940

CCTGGTATAAAAGAGGCGAGGGTCACTGATGCAGGACCTCCCGCAGCCGCCACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 350

CCTGGTATAAAAGAGGCGAGGGTCACTGATGCAGGACCTCCCGCAGCCGCCACCTCAACCCAGGAACAGAGCGAGGCGACGCCGCGGCACCTCTTCTCCGgtaagtgaga ... catttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaacccaaagtcttccgcagatagtaatgatatacggaatatcacatttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC
                     atagtaatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatctgtcttagaaatactaagtcaaatgttccgcattagcttgcaacccaaagtcttccgcagatagtaatgatatacggaatatcacatttggcagTTGATATTGATTATTTAGGCGAAGGGAAATGGCAACCGTTCCAGGGGATCTGATCTGGCAGGTTGTGAGGAAGAACAACTCCTTCCTTGTGAAGCAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - acccaaa