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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagtgcttctgttaatgacacatggacatatagacactggccataatttcccattgatctgcag

Basic information

species Zea mays
transcript GRMZM2G149994_T04
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149994_T04 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os04g42110.1 (Oryza sativa), 5'ss of exon 11
GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagtgcttctgttaatgacacatggacata-tagaca----ctggccataatttcccattgatctgcag
|||||||| ||||||| |||||| |||||||||||||||||||||||||||||| |||| |||||||||||||||| |||    |  |    || |   |  | |    |||||  | |||    |  |   |  ||| |  || | ||||||
GGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTCGATATGgtatcccgatctccctctccctctccctcacacatagcaaacaaaatcatgttctttttttcattttaactgcag

upper sequence: GRMZM2G149994_T04 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g31220.1 (Oryza sativa), 5'ss of exon 7
GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagtgcttctgttaatgacacatggacata-tagacactggccataat-------ttcccattgatctgcag
|||||||| ||||||| |||||| |||||||||||||||||||||||||||||| |||| ||||||||||| |||| |||    |  |    || |   |  | |    |||||  | ||| |   |||  |       || |  || | ||||||
GGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTTGATATGgtatcccgatctccctctccctctccctcacacatagcaaacaataatcatgttctttttttttcattttaactgcag

upper sequence: GRMZM2G149994_T04 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G13160.1 (Glycine max), 5'ss of exon 12
GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgt-----------ccttcagtgcttctgttaatgacacatggacatatagacac---tggccataatttcccattgatctgcag----------------
|||||| | || ||||  ||||| ||||||||  |||||||||||||||| ||  ||||||| |||||||| |||  |||            ||||   | | ||  | ||      || |  |  |   |    ||   | ||| |  ||  ||| || |                 
GGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTGgtgcaaaataatatcttcgacgatacttgtgattcagtttgtaacttgaattatacatgttaaaaatatatcaaggatttgtacatttacaataatgaaa

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|24934695|gb|CA452913.1|CA452913
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCCCCAGATGTGGAAGGCCGACCCGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|76015203|gb|DT942373.1|DT942373
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|211031499|gb|FL245298.1|FL245298
EST:     GTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|24773622|gb|CA408876.1|CA408876
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCCCCAGATGTGGAAGGCCGACCCGAGATTCTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|37391984|gb|CF633237.1|CF633237
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|211033356|gb|FL442938.1|FL442938
EST:     GCCCAAAAGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|67026000|gb|CO454749.1|CO454749
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|211031500|gb|FL245299.1|FL245299
EST:     GCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|24934696|gb|CA452914.1|CA452914
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGCCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|67018676|gb|CO447425.1|CO447425
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|24961608|gb|CA483609.1|CA483609
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGCCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|5296146|gb|AI783021.1|AI783021
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|33092600|gb|CF052594.1|CF052594
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAAATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|24773369|gb|CA408623.1|CA408623
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGCCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|24773164|gb|CA408418.1|CA408418
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGCCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
EST: gi|4609489|gb|AI600328.1|AI600328
EST:     GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG                         GTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC
genomic: GCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGC

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: 150

GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGCATCCATACACGGAAAATGAAGTTGGGAGAGGATGTAGATCTTTGGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGCATCCATACACGGAAAATGAAGTTGGGAGAGGATGTAGATCTTTGGAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGCATCCATACACGGAAAATGAAGTTGGGAGAGGATGTAGATCTTTGGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagt ... tgatctgcagGTGCTGTATGTCCCGCCACCAGATGTGGAAGGGCGACACGAGATACTACGCATCCATACACGGAAAATGAAGTTGGGAGAGGATGTAGATCTTTGGAAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGgtccttcagtgcttctgttaatgacacatggacatatagacactggccataatttcccattgatctgcag

- - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - -  GCTGCT