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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatccctttccaaatgtccttttcaacccgtcgtttttcttgcagatccttgtctaattgatgttatggtaacacagcctcatgttctttgtgctttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA

Basic information

species Zea mays
transcript GRMZM2G113726_T04
intron # 5
splice site 3'
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|50330988|gb|CO526114.1|CO526114
EST:     ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
EST: gi|51593066|gb|CV072212.1|CV072212
EST:     GTAAGAAGCAAGAAGTCATTAATCTTCTAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATTACTACGAGGGGTTTTATCGGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
EST: gi|211510692|gb|FL132928.1|FL132928
EST:     ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
EST: gi|60349121|gb|DN216094.1|DN216094
EST:     ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
EST: gi|71771227|gb|DR969164.1|DR969164
EST:     ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT
EST: gi|109179023|gb|EC379766.1|EC379766
EST:     GTAAGAAGCAAGAAGTCATTAATCTTCTAGGACATGTGACACCGTGCGAG                         AAGCACCATCGGAATTACTACGAGGGGTTTTATCGGACTCCAGTCAGTACT
genomic: ATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACT

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), 45 (downstream exon)
Score: 51

TGTGTATCTTATGTCAAACTTTTCTGTGCTTCATTGGTCAGCAATGACTTATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 111

TGTGTATCTTATGTCAAACTTTTCTGTGCTTCATTGGTCAGCAATGACTTATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 69

TGTGTATCTTATGTCAAACTTTTCTGTGCTTCATTGGTCAGCAATGACTTATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 40

TGTGTATCTTATGTCAAACTTTTCTGTGCTTCATTGGTCAGCAATGACTTATAAGAAGCAAGAAGTCATTAATCTTCAAGGACATGTGACACCGTGCGAGgtacatatcc ... ttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctaattgatgttatggtaacacagcctcatgttctttgtgctttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA
     aattgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatccctttccaaatgtccttttcaacccgtcgtttttcttgcagatccttgtctaattgatgttatggtaacacagcctcatgttctttgtgctttgacttcagAAGCACCATCGGAATCACTACGAGGGTTTTTATCAGACTCCAGTCAGTACTTTGGCGGTGAAGCATAACTTGCTTGTTACTGGTGGGTTTCATGGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG