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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA

Basic information

species Zea mays
transcript GRMZM2G452386_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g32850.1 (Oryza sativa), 3'ss of exon 9
-gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtca-tgcctgtaaactaaactgcgtcctcc------ctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
       |    |||||||  || |||      |  |||| | | | |||||  ||| |||||  |  ||   | |       ||||  ||| || |||||||| | | | | || || ||        ||   |          | |||   |||  | |  |||| |||||||||||| |||| |||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |||| || ||||
gtcgtggcacaaatctattaaattata------cattagaatgtct-tctcaacatgggataaaatgttca--tag-------ttgaagtatcttttttgctgtattaatacttgcaatctccgtaatttctgacgaataatcagtcaatgactttattta--ccttctccagGGTTCCTGCAGATATGCCTTTATATGACATACTGAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAGCCCAAAATTGTACCA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G33660.1 (Glycine max), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA--
                                                                                 |||||   ||  |      ||| |  || || |      ||||  ||| |   |||   |  || ||| |||    || |||||||||||  |||| |||||| | |||||||| |||||||||||||| |||||||| ||||||||||| ||||| || |||| || |    | |  ||| ||  
--------------------------------------------------------------------------------gtttgaccaatggtgccc-ttgtattttgtcttt----ctaactcagtcat---tgaactaagttattgttcataaattatccagGGTTCCAGCAGATATGCCTCTATATGATATCCTCAATGAGTTTCAAAAAGGAAGCAGTCATATGGCAGCTGTAGTTAAGGTTATA--AGAGAGAGAAACAAC

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G38600.1 (Glycine max), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttc--cagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                                       |||        || |   ||||  | |  ||| |  |   |  || ||||    |      ||    |||  || | ||    |   | |   ||||||||| ||||| |||||| | ||||||||||| |||||||| || || |||||||||||||||||||||||||| |||||||     |||    ||  |
-----------------------------------------------------------------------gtgtgctttcctttattaatttattcttatgttttttttttccaatctaatagtcaagtatcc----aaagtttgtggacgggtttatatgtacagGGTTCCATCAGATATGCCTCTCTATGATATACTAAATGAGTTCCAAAAGGGAAGTAGTCATATGGCTGCTGTTGTTAAGGCTAGGGGAAAAGGCAAAGAA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G02110.1 (Glycine max), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                                     | |||   |  |||    || | ||||    | | |  |   |  |||||||  ||     |  |  |    | | |  |     |   | | ||||||||| ||||| |||||| | ||||||||||| |||||||| || || |||||||||||||||||||||||||| |||||||     |||    ||  |
---------------------------------------------------------------------gtgtgcttgtctttattaatttattctcatgtttttttttttttcaaactaa-ttgtcaagtatccaaagtttgtgtacggggtttatatgtacagGGTTCCATCAGATATGCCTCTCTATGATATACTAAATGAGTTCCAAAAGGGAAGTAGTCATATGGCTGCTGTTGTTAAGGCTAGGGGAAAAGGCAAAGAA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G11030.1 (Glycine max), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcc-tccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                                 |||  |      || | |     || |||   | || ||| ||   |  ||  | ||   |     ||  | ||   | |  ||  |   | | ||| ||| ||||| ||||| |||||| | ||||||||||| |||||||| || || || ||||| ||||||||||||||||| | |||||     |||    || ||
--------------------------------------------------------------atctctttaacatttgattct---attaatttacattct-tgttatttttaaaattttaatgtcaaatatcagtaatttgtgtaattttttgttacatttacagAGTTCCATCAGATATGCCTCTTTATGATATACTGAATGAGTTCCAAAAGGGCAGTAGCCATATGGCTGCTGTTGTTAGGGCTAGGGGGAAAGGAAAAACA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G03270.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                   |||| |  | || | |  ||||    |    ||||  || |          | | |||  | || |   || |      ||||  ||| ||            | | ||||||||||||| ||||||||||| ||||||||||| |||||||||||||| || ||||| ||||| |||||||| ||||| || |  |||   |||  | ||   
---------------------------------------------------gtatatc-tgacttccctgagtataag----ttgacctactc--------atattatgtttctagatagaagtataagttccc--atacat------------tgcctttccagGGTTCCATCAGACATGCCATTGTATGATATCCTCAATGAGTTTCAAAAGGGAAGCAGTCACATGGCTGCAGTTGTCAAAGTCAAAGACAAAGATAAAAAG

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G14230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                             ||||    || |  ||   | ||      ||    |||| | ||  |||| ||       |||  |||| ||  |||    || |    ||           |||| |||  |||  |||||||||  |  | |||||| |||||||||| || ||||||||||| ||||| || ||||| |||||||| |||||||||| |||    ||||   ||   
---------------------------------------------gtcttgtcat-tattattatgctt-----gctatattttcatattatttcctta----agcatctctgtgaa--aaatgaagttcctgttg-----------tgattaatgatttaacagGGTTCCGGCTAATATGCCTCTGTATGATATTCTGAATGAGTTTCAAAAAGGGAGCAGTCACATGGCTGCAGTTGTGAAGGTTAAGGGGAAAAGCAAAGGT

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G14240.2 (Arabidopsis thaliana), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                               |||||    |  |    |||| |  |    ||||| || |        |||| | | ||    ||      | ||  || || |     |||  ||    ||||||||  | || |||||| | ||||||||||| ||||||||||| || ||||| ||||| |||||||| |||||||||| |||    ||||   ||   
---------------------------------------------------------------gttctgccattacca--ttttaacctccagtctttactat------tatgtagaatgaa----gtttcgtattattgatgttat-----aatgtttgaatagGGTTCCAGCTGATATGCCTCTCTATGATATACTGAATGAGTTTCAAAAGGGAAGCAGTCACATGGCTGCAGTTGTGAAGGTTAAGGGGAAAAGCAAAGTC

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0104g00300.t01 (Vitis vinifera), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                                               | | |   ||  ||| ||| || | | | || | |    | |  |   |  |       |   | |||  ||  ||  || |||||||||||  |||| ||||||||||||||||| ||||| || ||||| || ||||| ||||| ||||| ||||| ||||||| ||||   ||||   |    
---------------------------------------------------------------------------gtatgctattttatcgtttatttactttttta-gcttttgtctttatttttctattaaaaagcatgaaatttc-atgcattgttatccagGGTTCCGGCAGATATGCCTTTGTATGATATCCTCAACGAATTTCAAAAGGGAAGCAGTCACATGGCAGCTGTAGTGAAGGTTAAAGGAAAAAACAAGAAT

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S18_210V6.1 (Physcomitrella patens), 3'ss of exon 9
gtacacccttcatctattggataatattcttgctctagactc-tttgtctcagtatgtgataac-gttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                     ||| | ||| |   | |      ||   | | ||| ||  |  |||||| || |      |  |     || |||  | | ||| |             |||| |   |  | ||  ||        |||||| ||    |||||||| || ||||| || || ||||| |||||||||||| ||||||||||||||||||| |||   | |||||| | ||    |  |
------------------------------------ggacccatttcttctaattcacattattaggtttcgggta-ctcagttttaaggt-----ttacggaacatcctgc--ggagactga-------------tgatgagggtgctgga--aa--------cagGGTGCCAGAGGACATGCCATTATATGACATTCTGAATGAATTTCAGAAAGGAGGTAGTCATATGGCTGCTGTAGTGGCAGTTAAACCGAGAAAGAGAAAA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S294_17V6.1 (Physcomitrella patens), 3'ss of exon 10
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagt-ggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                        | ||   |  || || | |||    ||||  || |||    ||      | | |     || |   |  | | |   | || | | |  ||||| |   ||      |||||| ||    ||||||||  | || |||||| | |||||||||||||||||  |||| |||||||||||||| |||   | |||   |   |    |  |
--------------------------------------------------------ttatg-tgcgcttgacttggcaagtttttatgagattcgggtttgaaatttagg---agaagccctatggagact--catggtca-tgattttggt---tctggagacagGGTGCCAGAGGACATGCCACTCTACGATATATTAAATGAGTTTCAGAAAGGTGGTAGCCATATGGCTGCTGTAGTGGCCGTTAAGAGTGGGAGAAGAAAA

upper sequence: GRMZM2G452386_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05730 (Selaginella moellendorffii), 3'ss of exon 6
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                                                                                                    ||| |  ||   | |   |   |  ||   |||     |   |   ||| || ||| |||||||||||||||| ||||| || || ||||| ||||||||||  || || ||||| ||||| ||||| || ||    ||||   | |||
------------------------------------------------------------------------------------------------------------------gtacttag-tgttacttttgtatgaggtacaattgg--ggtttctgctcagAGTACCTGCAGACATGCCTTTGTACGATATCCTGAACGAGTTCCAGAAAGGAAACAGCCACATGGCAGCTGTGGTGAAAGCGAAGATGAAAAGGAAGCCA

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|32868728|gb|CF008410.1|CF008410
EST:     GCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAG                         GGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGG
genomic: GCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGG
EST: gi|33098468|gb|CF058428.1|CF058428
EST:     GCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAG                         GGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGG
genomic: GCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGG

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), 46 (downstream exon)
Score: 143

GTGAAGAGTCTTTTGACTGTTCGTGCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GTGAAGAGTCTTTTGACTGTTCGTGCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

GTGAAGAGTCTTTTGACTGTTCGTGCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 239

GTGAAGAGTCTTTTGACTGTTCGTGCTGAAACGGAGACGCCGGTTAGTGCTGTTTCAATTAGAAGGATTCCAAGgtacaccctt ... ccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA
                                            tccttttcc  CT-rich tract
                        tgataaatatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacccttcatctattggataatattcttgctctagactctttgtctcagtatgtgataacgttctcgagtggcggagttttgagatattttctttgctgtgtcatgcctgtaaactaaactgcgtcctccctgataaatatttttgatcaatccttttccagGGTTCCTTCAGACATGCCTTTGTATGATATACTCAATGAGTTTCAGAAAGGAAGTAGTCATATGGCTGCTGTTGTGAAGGCTAAACCTAAAACTGAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT