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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtcgagtaaaataaactgaaggtttcacacatcatgtatttgtattgtattcataaagaaactgcatgcctcactgccaatctttgaccatttccag

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 8
AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtcgagtaaaataaactgaaggtttcacacatcatgtatttgtattgtatt------------cataaagaaa----------ctgcatgcctcactgccaatctttgaccatttccag
||||||||| ||||||||||||||||||||||| || |||||| |||||| ||       ||  |||||| |||||||  ||  |||| | || | |||  |||            ||| || |||          || |||  || |||  ||||||||| ||||||||||
AACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTGgtaaaat-------aatctaaactaaaggtttttca-gtcatatcttagcattaaattagatgagccaagcatgaacaaattcatctgtacttcatagctaactaacaatctttgtccatttccag
















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|149076952|gb|EE165608.2|EE165608
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|71322126|gb|DR797758.1|DR797758
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCT
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCT
EST: gi|37400724|gb|CF637721.1|CF637721
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|113702575|gb|EE680079.1|EE680079
EST:     TTTTTCCTATTTTACATG                         ATTCATATAATGTTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTC
genomic: TTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTG-TTTTTCCTATTTTAAATG                         ATTCATATAATATTCTG
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTG
EST: gi|78112245|gb|DV530639.1|DV530639
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|78180134|gb|DV550507.1|DV550507
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|76927276|gb|DV171212.1|DV171212
EST:     AACTGAGAGCGCTTGGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCGGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|5847119|gb|AW000198.1|AW000198
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|60396504|gb|DN229373.1|DN229373
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|32851209|gb|CD990890.1|CD990890
EST:     GGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: GGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|37374257|gb|CF623473.1|CF623473
EST:     TGAGAACTGAGAGCGCTTTGAAGTTGGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTC
genomic: TGAGAACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|78081464|gb|DV509876.1|DV509876
EST:     TTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: TTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|76289052|gb|DV028620.1|DV028620
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|5343187|gb|AI795372.1|AI795372
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATCTTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTTCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     AACTGAGAGCGCTTTGAGGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCT
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCT
EST: gi|8551590|gb|BE128935.1|BE128935
EST:     AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG                         ATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC
genomic: AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTC

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), 34 (downstream exon)
Score: 559

AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 538

AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 494

AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 843

AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtc ... ccatttccagATTCATATAATATTCTGTGTGTGGGCAGCTGTGGCTCCTCCATTCCCTTTCAAAGGAAAATCTTTGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATGgtaagatgtcgagtaaaataaactgaaggtttcacacatcatgtatttgtattgtattcataaagaaactgcatgcctcactgccaatctttgaccatttccag

- - - - - -  TTGAAG