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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcccgtaaaacattttgtgtggtttgtataaaatccaaagctacatttcatgaaagtaatgaagtataccttttgtaaatgtttctccacattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 3
-aatcccgtaaaac--attttgtgtggtttgtataaaatccaaagctacatttcatgaaagtaatgaagtataccttttgtaaatgtttctccaca-ttatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG
 || |   | |  |  |  |      | | |  | || |    |  ||||||| ||  |||| | |   | || ||    |  || ||| |  | | | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| ||||||||| | |||||  |||| |||||||| ||||||||||| |
aaaacatttgaccctaacatcaaagtgatagcctgaagtt---acttacattttatataagtgaagcttt-taactgaaatgcatctttgtttataatcatcagGTTTCAAGTAAAGAAAAAACAATTCTTCCGCAATTTTATGACAATTATTTTATTTGGTGCTGTGGGGACATTGATATCCTTTGTGATAATCTCTCTAG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 3
aatcccgtaaaacattttgtgtggtttgtataaaatccaaagctacatttcatgaaagtaatgaagtataccttttgtaaatgtttctccacattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG
                  ||  | | | | ||   |  | |     |||||||||||  | ||||        ||    ||    | |     ||| ||||||||| || ||||| |||||||| || |||||||| || || ||||| || |||||||||||||| ||||| ||||| ||||| || |||||  |||
------------------gtaagttcttttta---tataga-----atttcatgaaaa-attgaaagtcggaattgagtaacacatttttttgtta-cagGTTTCAGGTTAAGAAGAAGCAATTTTTTCGCAACTTCATGACCATTATGTTATTTGGTGCTATTGGAACTCTCATTTCATTTGTTATCATCTCATTTG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 2
aatcccgtaaaacattttgtgtggtttgtat-aaaatccaaagctacatttcatgaaagtaatgaagtataccttttgtaaatgtttctccacattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG
|| |          |      ||   || || |||||    || ||  | || |      |   | || |  ||  | | |   ||| | |   |  ||||||| || ||||| || ||||| || ||||| |||||||| ||||| || ||||||||||||||||| || ||||| |||||||  || || ||||| |
aagcgtactttctctccatattgacatgcattaaaatgtgcagttatttatcttttcttgaggtaggttttgctgatttgataattttttcttgt-gtcagGTTCCAGGTAAAAAAGAAGCAGTTTTTCCGAAACTTTATGACAATCATATTGTTTGGTGCTATTGGTACACTGATATCCTTTGGCATTATATCTCTAG

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|71320091|gb|DR796800.1|DR796800
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|211214877|gb|FK947155.1|FK947155
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACGATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|211214880|gb|FK947158.1|FK947158
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGC
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGC
EST: gi|78078433|gb|DV506847.1|DV506847
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACGATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|71327380|gb|DR800303.1|DR800303
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|67026824|gb|CO455573.1|CO455573
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|91872698|gb|EB402655.1|EB402655
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|211212317|gb|FK947152.1|FK947152
EST:     AGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGTG                         GTTTCAAGTAAAGAAAAAGCAATTCTTTCCGCA-CTTTATAACGATTATT
genomic: AGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCG-Ggtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTT-CCGCAACTTTATAACAATTATT
EST: gi|76915777|gb|DV166118.1|DV166118
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
EST: gi|78118702|gb|DV537086.1|DV537086
EST:     GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGG                         GTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT
genomic: GAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTT

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: 152

TCATCCTGCTGGTTACTAATGGGACAAACTCACGCATTCTTGTGTTCAGCGAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

TCATCCTGCTGGTTACTAATGGGACAAACTCACGCATTCTTGTGTTCAGCGAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

TCATCCTGCTGGTTACTAATGGGACAAACTCACGCATTCTTGTGTTCAGCGAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

TCATCCTGCTGGTTACTAATGGGACAAACTCACGCATTCTTGTGTTCAGCGAGGACCTGTTTTTCATATATTTACTTCCGCCGATAATCTTCAATGCCGGgtgagtctgc ... acattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcatgaaagtaatgaagtataccttttgtaaatgtttctccacattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG
                                      tttctccac  CT-rich tract
                           ttttgtaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcccgtaaaacattttgtgtggtttgtataaaatccaaagctacatttcatgaaagtaatgaagtataccttttgtaaatgtttctccacattatcagGTTTCAAGTAAAGAAAAAGCAATTCTTCCGCAACTTTATAACAATTATTTTGTTTGGTGCTATTGGGACTCTGATTTCCTTTGTAATAATCTCTCTTG

- - - gtaaaaca
- - - - - - - - - - - - - - - - - - - - agctaca
- - - - - - - - - - - - - - - - - - - - - - - - - catgaaa