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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgctcattatcttccccttggtttttctagtatggaaacagcagatggtctcgattttgtatttttgtttcctttctgaaatgatcctgataa...

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G492252_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 5'ss of exon 8
TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgctcattatcttccccttggtttttctagtatggaaacagcagatggtctcgattttgtatt-tttgtttcctttctgaaatgatcctgataa---
|| ||||| ||| || |   |||||||  | ||||| |||||||||||||| |||||| | ||||||||||| |||||||||||||||||| |||| |||||||||||  | | ||   |   |||  |||||     ||| | ||   | ||  ||| ||  |||| || ||||| |     |   |     | | ||     
TGCAACTGACAACACCCTGGAGGATGAGTTGACATGCAGTGTTTGCTTAGAACAAGTCGTTGTGGGTGATCTATTGAGAAGCCTACCATGCCTGCACCAGgtaatcattat-actagaattatctt--ttttttagacatgtatactaga-atcatcttgagcttgttttctttgtatgacagcaatagcaggctttatttcct
















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|78074674|gb|DV503108.1|DV503108
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|60359234|gb|DN226207.1|DN226207
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|89760189|gb|DY688710.1|DY688710
EST:     TGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: TGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|211241084|gb|FL183326.1|FL183326
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|91052810|gb|EB163228.1|EB163228
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|78123225|gb|DV541609.1|DV541609
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|110517661|gb|EE022248.1|EE022248
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|211238857|gb|FL183325.1|FL183325
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|78092370|gb|DV520744.1|DV520744
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|88758240|gb|DY542381.1|DY542381
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|88754551|gb|DY538692.1|DY538692
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|93014827|gb|EB640347.1|EB640347
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|7135740|gb|AW498241.1|AW498241
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|211111576|gb|FL459318.1|FL459318
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|16922425|gb|BM075574.1|BM075574
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|71774881|gb|DR972759.1|DR972759
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|60352872|gb|DN219845.1|DN219845
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|86467860|gb|DY234230.1|DY234230
EST:     AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|101381640|gb|EB812877.1|EB812877
EST:     GGTGGGTGATTTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: GGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA

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: 47 (upstream exon), 46 (downstream exon)
Score: 65

TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTCAGTGATGGGTGGCATGCCACAGGCAACGGTG


Block sizes: 49 (upstream exon), 15 (downstream exon)
Score: 3

TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTCAGTGATGGGTGGCATGCCACAGGCAACGGTG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 8

TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTCAGTGATGGGTGGCATGCCACAGGCAACGGTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 18

TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgc ... tgttttgcagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTCAGTGATGGGTGGCATGCCACAGGCAACGGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAACTGGCAAAACTCCACAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCATGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatgctcattatcttccccttggtttttctagtatggaaacagcagatggtctcgattttgtatttttgtttcctttctgaaatgatcctgataa

- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC