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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggtttcttttcaccagttctttttaaatcattcacttctcgttttacttcttatttttttttgttttaatgttttgatatatatatcttatttagtatacttaattatgtattgctttgatttcagtggcttatatactgtatgttgtttttag

Basic information

species Zea mays
transcript GRMZM2G111510_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111510_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g53560.1 (Oryza sativa), 5'ss of exon 10
GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggtttct---tttcaccagttctttttaaatcattcacttctcgttttacttcttatttttttttgttttaatgttttga-tatatatatcttatttagtatacttaattatgtattgctttgatttcagtggcttatatactgtatgttgtttttag
 |||||||||||| |||||||||||| | || |||| |||||||||||  ||||||  |||||| ||||||| || ||  |||||||| | ||| |    || || |||||||||      ||  |  | | |||  |   | | | | | |  |||  |  |  || | |||  | ||   ||                                                               
TGTTGGTGCAGACAAGTGGTCTTTACTGTATGAATCGATTCCAGAAAAGCTGCAAATCCTGTACAATGATGGCTATAAATTGgttagttgctttttagtctttacaagttcttttgggcctat--aactgtagttccatcacgtctctctgtacgttgcatcgaattaagtatgcacatagaat---------------------------------------------------------------
















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|6563667|gb|AW231394.1|AW231394
EST:     AATCAATTCCAGAAAAATTGCAAAGCCTGTCCGATGATGGTTCCAAGCTG                         GTCATATTCNCCAATGAGTCAACCATTGAGCGCTGGAAGACCAAGCGNCAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|32835438|gb|CD975116.1|CD975116
EST:     GTACAATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: GTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|78088731|gb|DV517124.1|DV517124
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60359551|gb|DN226524.1|DN226524
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|71432125|gb|DR813175.1|DR813175
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60341580|gb|DN208553.1|DN208553
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|211443974|gb|FL182596.1|FL182596
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|71759141|gb|DR957078.1|DR957078
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|78088730|gb|DV517123.1|DV517123
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCCCCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60336621|gb|DN203594.1|DN203594
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|83279155|gb|DV943163.1|DV943163
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|91053260|gb|EB163678.1|EB163678
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|71316663|gb|DR795006.1|DR795006
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60342489|gb|DN209462.1|DN209462
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|32833310|gb|CD972988.1|CD972988
EST:     ATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: ATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60401163|gb|DN233970.1|DN233970
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|37426318|gb|CF650911.1|CF650911
EST:     GATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: GATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|60351350|gb|DN218323.1|DN218323
EST:     AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: AATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
EST: gi|33092918|gb|CF052912.1|CF052912
EST:     ATGATGGTTACAAGCTG                         GTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA
genomic: ATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAA

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: 115

GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAACAAGCTGTTGACTCCAAAGTTGGCCGCCTTGATAACTTTATTGAATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAACAAGCTGTTGACTCCAAAGTTGGCCGCCTTGATAACTTTATTGAATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAACAAGCTGTTGACTCCAAAGTTGGCCGCCTTGATAACTTTATTGAATGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 28

GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggt ... ttgtttttagGTCATATTCACCAATGAGTCAAACATTGAGCGCTGGAAGAACAAGCGACAACAAGCTGTTGACTCCAAAGTTGGCCGCCTTGATAACTTTATTGAATGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTGgttagtaggtttcttttcaccagttctttttaaatcattcacttctcgttttacttcttatttttttttgttttaatgttttgatatatatatcttatttagtatacttaattatgtattgctttgatttcagtggcttatatactgtatgttgtttttag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG