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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagctgtattgcttggatgaattcatttatctgggtttttttaatcatggagcctacaatatccaccagtggtatgacctatgctggatgatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT

Basic information

species Zea mays
transcript GRMZM2G022563_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 3'ss of exon 1
ccagctgtattgcttggatgaattcatttatctgggtttttttaatcatggagcctacaatatccacca--gtggtatgacc---tatgctggatgata--ttacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT
        | || |||||   | || || |||||   ||||||  | | |||| ||| | |||   | |  |||| |||| |   ||   |  |||  |   |  ||||| || |||||||||||||| ||| ||||||| ||||| ||||  ||| | |||||||||||||||||||||||||| || ||||||||||||||||||
-------cactggttggacttactcgttgatctgcactttttttgttaaggagtctaaattattttcgactgtggaatgaactcataaaattaatgggaacctgtagGGTCGTCGGTATGGGTTCAAAACTCATTGGATGCGGATCGGCCACTCCATCGCTTAGCGTTTCAAATGATGACCTTTCTAAAATAGTTGAAACATCAGAT
















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|149099166|gb|EE185191.2|EE185191
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCTCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|71430696|gb|DR811746.1|DR811746
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|76921158|gb|DV168472.1|DV168472
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|71446997|gb|DR828047.1|DR828047
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|89756348|gb|DY686398.1|DY686398
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|71429949|gb|DR810999.1|DR810999
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|76291106|gb|DV030674.1|DV030674
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|9732483|gb|BE511235.1|BE511235
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|149095842|gb|EE181493.2|EE181493
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|149105057|gb|EE290536.2|EE290536
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|78121840|gb|DV540224.1|DV540224
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|148935022|gb|EC879064.2|EC879064
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
EST: gi|101397488|gb|EB820667.1|EB820667
EST:     GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAG                         GGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC
genomic: GTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAAC

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), 48 (downstream exon)
Score: 59

CGCAGCCCGTGACGCTGCCACCGCCCCAGCTCCGGTGCTGCGCGTCCACCGTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 37

CGCAGCCCGTGACGCTGCCACCGCCCCAGCTCCGGTGCTGCGCGTCCACCGTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT


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

CGCAGCCCGTGACGCTGCCACCGCCCCAGCTCCGGTGCTGCGCGTCCACCGTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 84

CGCAGCCCGTGACGCTGCCACCGCCCCAGCTCCGGTGCTGCGCGTCCACCGTCGACGATGGCGTGGTGTCCGCTGCGGCTTCCAAGCCCCGCCTCCCCAGgtaacgccgg ... gatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatggagcctacaatatccaccagtggtatgacctatgctggatgatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT
                                           atgatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagctgtattgcttggatgaattcatttatctgggtttttttaatcatggagcctacaatatccaccagtggtatgacctatgctggatgatattacagGGTGGTTGGTATGGGTTCAAAGCTCGTTGGATGTGGATCAGCCATCCCAACACTTAGCGTTTCAAATGATGACCTTTCGAAGATAGTTGAAACATCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
ccagctg
- - - - - tgcttgg
- - - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - gcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg