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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgcctgtgactgaagaaattgcatctatattgaccttgttgtattttggccacaactggatgctttagctcctgactttttttgttcttttcag

Basic information

species Zea mays
transcript GRMZM2G174830_T01
intron # 3
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|74242321|gb|DT650235.1|DT650235
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|78114801|gb|DV533189.1|DV533189
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|71433192|gb|DR814242.1|DR814242
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|211353516|gb|FL063245.1|FL063245
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|211351121|gb|FL063242.1|FL063242
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATTGACGCGACTATGACGTCAG
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAAT-GACGCGACTATGACGTCAG
EST: gi|211351119|gb|FL063240.1|FL063240
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTTC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|78081398|gb|DV509810.1|DV509810
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTG
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTG
EST: gi|211351120|gb|FL063241.1|FL063241
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGTGACTATGACTTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
EST: gi|211351122|gb|FL063243.1|FL063243
EST:     ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAAT                         GGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC
genomic: ACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCC

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), 44 (downstream exon)
Score: 47

GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCCTACCGTTGCTCGTCCGATACGTTTGATCCCCAAGGACGCACTTTCGATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 24

GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCCTACCGTTGCTCGTCCGATACGTTTGATCCCCAAGGACGCACTTTCGATA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 17

GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCCTACCGTTGCTCGTCCGATACGTTTGATCCCCAAGGACGCACTTTCGATA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 51

GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgc ... ttcttttcagGGGAATGACGCGACTATGACGTCAGTAAGTGGCCACGCAGATGATCTTTCCTACCGTTGCTCGTCCGATACGTTTGATCCCCAAGGACGCACTTTCGATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGAAGGGTGACCCAAGTGATCCTTTGAACAGCTCCAGGAGTTCTGTTGGTCCCAGTAAACACCTCAGTCTGCCCAATgtgagcctgcctgtgactgaagaaattgcatctatattgaccttgttgtattttggccacaactggatgctttagctcctgactttttttgttcttttcag

- - - - - - - - - - - - - - - CAGCTC