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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatatgtgatgacctgtccattccgggacactagaatttctaccatatcatcctcatcttccccgttgctgctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 3'ss of exon 21
--gtaagcatatgtgatgac-ctgtccattccgggacactagaatttctaccatatcat-cctcatcttccccgttgctgctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAA-TAAGGCATCAAGATCA
   |     | | |       || |  |||  | ||   | ||||  |    |  | |   ||||||| || | ||||| |      |||||||||||||||||||||||||  | ||  | || || || ||||| ||||||||||| || || |||||||| || |||||| ||| ||    |   | 
gtattgtggtttatcgcactgcttttgattatgagatgtttgaataccccttacctgaaatctcatctcccgcattgctac------agGTGTGGTACGAGTGGGCTGTGACGGCACCTTCTCCATCACCAATCCATAACAGCAATGGTCGATCATATTGGGTCGGCCTATAAGTAAAGCCATGAAGCC-
















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|20803221|gb|BQ294271.1|BQ294271
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCT
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCT
EST: gi|40336264|gb|CK370334.1|CK370334
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|5005784|gb|AI711846.1|AI711846
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|60345333|gb|DN212306.1|DN212306
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|78117238|gb|DV535625.1|DV535625
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|32944743|gb|CF049562.1|CF049562
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|20337078|gb|BQ172708.1|BQ172708
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCA
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCA
EST: gi|71300981|gb|DR786519.1|DR786519
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|211483574|gb|FL225319.1|FL225319
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACDAAG                         GTGTGGTWCGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|21891446|gb|BQ744659.1|BQ744659
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|31558383|gb|CD527595.1|CD527595
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|37392891|gb|CF633698.1|CF633698
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|60399845|gb|DN232655.1|DN232655
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|18177852|gb|BM379062.1|BM379062
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|87155574|gb|DY400363.1|DY400363
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|91876144|gb|EB406101.1|EB406101
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGNNNNNNNGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|31558384|gb|CD527596.1|CD527596
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|33468107|gb|CF245156.1|CF245156
EST:     AGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGGCCCCCGCGAAG                         GTGTGGTACGAGTGGGCTGT
genomic: AGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTG-CCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGT
EST: gi|37398225|gb|CF636423.1|CF636423
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|71311076|gb|DR791852.1|DR791852
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|91048537|gb|EB158955.1|EB158955
EST:     AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC
EST: gi|211352737|gb|FL476231.1|FL476231
EST:     AAGGGTCTCCTATAGAAGTACACTTCTGGCGGTGCTGTGCCCCCACAAAG                         GTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCATCGCCGATCCACAAC
genomic: AAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAAC

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), 49 (downstream exon)
Score: 185

GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAGgtaagcatat ... gctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacactagaatttctaccatatcatcctcatcttccccgttgctgctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA
      tagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatatgtgatgacctgtccattccgggacactagaatttctaccatatcatcctcatcttccccgttgctgctgctgcagGTGTGGTACGAGTGGGCTGTGACTACGCCGACCCCGTCGCCGATCCACAACAGCAATGGCCGGTCCTATTGGGTTGGTCTATAATAAGGCATCAAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA