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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtgatatattgtaaatttgggcatctctgtctccacacagaaggttttatggtgcatttctgtgttctctaaatatttctgccaacatatctt...

Basic information

species Zea mays
transcript GRMZM2G045366_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045366_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 9
GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtgatatattgtaaatttgggcatctctgtctccacacagaaggttttatggtgcatttctgtgttctctaaatatttctgccaacatatctt----------------------------
|||  ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||| |||||||||| |||||||   ||| |    || ||  ||  | ||  ||||  |   |   |  ||    |    |   |     | |||  |      |    || |    ||                            
GTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGgtaaaa-gtgttgctatgcaacattctgtattcctgtgccactatgaactgtaaagtaaaactgctgaacctactcccagagccccctagaagaccagtttttgtactgatattccaaacattttcag

upper sequence: GRMZM2G045366_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G58760.1 (Arabidopsis thaliana), 5'ss of exon 9
GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtgatatattgtaaatttgggcatctctgtctccacacagaaggttttatggtgcatttc-tgtgttctctaaatatttct------gccaacatatctt----------------------------
|   |||| |||||||||| ||     | ||||||||||||||||| ||||| ||||| ||||| |||||| | ||  | || |||||||   || ||  |  |     ||  |  | ||| |    | |   ||  |  |  ||   |     | | |   |  ||| ||  |      |  |||| |   |                            
GGCGATATATGGCTCCAGAGGTTTATAGGAATGAAGAGTATGATACAAAAGTAGATGTATTCTCTTTCGCTTTAATCTTACAAGAGgtaaa--gtaatcgagagagctattaagtttttctattcatagagtaaaaatcctccggcttaaacaatttataaacagaatgttgttttgtgggttaacagaatgttgttttgtgggttaacaaaacctaacag
















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|60344873|gb|DN211846.1|DN211846
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|32858352|gb|CD998033.1|CD998033
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ACGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|148965330|gb|EE016132.2|EE016132
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|211486462|gb|FL339896.1|FL339896
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|86472639|gb|DY239009.1|DY239009
EST:     TCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATCCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: TCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|76287393|gb|DV026961.1|DV026961
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|71760920|gb|DR958857.1|DR958857
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|71307029|gb|DR789668.1|DR789668
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|76291779|gb|DV031347.1|DV031347
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
EST: gi|74234286|gb|DT642200.1|DT642200
EST:     AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG                         ATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG
genomic: AGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAG

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), 43 (downstream exon)
Score: 82

GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAGAAGGCACATAATTCTAAAGAAAGGCCTCCTTTTCGAGCTCCTCCAAAGC


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

GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAGAAGGCACATAATTCTAAAGAAAGGCCTCCTTTTCGAGCTCCTCCAAAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAGAAGGCACATAATTCTAAAGAAAGGCCTCCTTTTCGAGCTCCTCCAAAGC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 154

GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtg ... actgttgcagATGATTGAAGGATGCCTTCCTTATTATGATAAGAAAAATGATGAAATTGAGAAGGCACATAATTCTAAAGAAAGGCCTCCTTTTCGAGCTCCTCCAAAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAGgtaagttgtgatatattgtaaatttgggcatctctgtctccacacagaaggttttatggtgcatttctgtgttctctaaatatttctgccaacatatctt

- - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA