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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaattttatctggtgctagttggttagccatactcatatcatttgtttgcaattgcatataaaaaatgatcatggtgtacatgtatatgtattt...

Basic information

species Zea mays
transcript GRMZM2G032944_T02
intron # 4
splice site 5'
intron type U2

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|211229014|gb|FL455773.1|FL455773
EST:     TGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|71765663|gb|DR963600.1|DR963600
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGANCATA-TGCCAACTACC
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGA-CATAATGCCAACTACC
EST: gi|149085004|gb|EE174514.2|EE174514
EST:     AATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: AATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|74246084|gb|DT653998.1|DT653998
EST:     TTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|78124011|gb|DV542395.1|DV542395
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|149085005|gb|EE174515.2|EE174515
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|71448268|gb|DR829318.1|DR829318
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|76914812|gb|DV165698.1|DV165698
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAA
EST: gi|31355055|gb|CD439412.1|CD439412
EST:     TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCAT
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCAT
EST: gi|71438631|gb|DR819681.1|DR819681
EST:     TTCTTGGAGAGAAACAATGTTGTGCTGGTGGCATGGATTTTATTACCATG                         ATATTCACACTGTCAGCCATACCCCTCGACATAATGCCAACTACC
genomic: TCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACC

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: 41 (upstream exon), 49 (downstream exon)
Score: 32

ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAACAATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 49

ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAACAATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 18

ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAACAATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 22

ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaat ... tcattggcagATATTCACACTGTCAGCCATACCCTTCGACATAATGCCAACTACCATAGAACAATGTGTTTCTGTTCTGAAACCAGGCGGCCTTCTTCTTTTTAGGGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCAAGTCACCATGGAATTAGAGAAGAGCACCCAGTCTTCCTTGGAGAGAACCAATGTTGTGCTGGTGGCATGGATTTTATTACCATGgtagattaattttatctggtgctagttggttagccatactcatatcatttgtttgcaattgcatataaaaaatgatcatggtgtacatgtatatgtattt

- - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA