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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttcctacctctatttttccgcttggtttgaagtgattaattacatttttttgggtttacataaaattcttccaattctccttgcattctttgc...

Basic information

species Zea mays
transcript GRMZM2G090338_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 4
GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttcctacctctat-ttttccgcttggtttgaagtgattaattacattttttt---gggtttacataaaattcttccaattctccttgcattctttgc
||| ||||| ||||| |||||||| |||||||| |||||||||||||||||||| |||| ||| ||||| ||  |||||||||| ||| ||||||||||||||||||||||| |   ||| |  |   | |||| || |   || || ||  ||    |    |  || | |  |||  |   ||| ||  |    || |||  
GGAAGTTAGCATTACTCCAAACCAGAATCTTATCTTATGTGGGATTGATCAAGCATGGAAAGATCCCATCACAGCAGCTCTTGCTCAATCTGGCCTGCTGgtaagatttccttcgcttatatcatatccctggtctgtaacaatgaaatatgttgccctccatgagttccctgtaatatta--aatccttgtaagcttattt--
















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|32840970|gb|CD980651.1|CD980651
EST:     AAGCATGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCTTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|211330974|gb|FL100736.1|FL100736
EST:     AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAG-ATGTCGACCCCCTGAA
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAA
EST: gi|13562272|gb|BG550492.1|BG550492
EST:     AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|67030464|gb|CO459213.1|CO459213
EST:     AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|71330578|gb|DR802057.1|DR802057
EST:     AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|47961924|gb|CN844633.1|CN844633
EST:     AAGCATGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCTTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|211330976|gb|FL100738.1|FL100738
EST:     AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|33091872|gb|CF051866.1|CF051866
EST:     AAGCATGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCTTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|32840868|gb|CD980549.1|CD980549
EST:     AAGCATGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCTTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC
EST: gi|32834834|gb|CD974512.1|CD974512
EST:     AAGCATGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTG                         GAACCGAAGGATGTCGACCCCTTGAATTTAACTGCCATGGCATGCCCTGCC
genomic: AAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCC

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: 615

GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2751

GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3475

GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1006

GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttc ... atgtatatagGAACCGAAGGATGTCGACCCCCTGAATTTAACTGCCATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGTTAGTATTACCCCAAACCAAAATCTTATTTTATGTGGGATTGATCAAGCGTGGAGAGAACCCATAACTACAGCTCTTGCACAAGCTGGCCTGCTGgtaagatttcctacctctatttttccgcttggtttgaagtgattaattacatttttttgggtttacataaaattcttccaattctccttgcattctttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataaaa