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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttttgtggtcattcttgatgttgtacttcctctgtcccagaatgataagcatagtttgtataggaaaaagtcaaatttagaattttatttccc...

Basic information

species Zea mays
transcript GRMZM2G049141_T02
intron # 13
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|211176318|gb|FL281704.1|FL281704
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTA
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTA
EST: gi|211174649|gb|FL281699.1|FL281699
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCT
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCT
EST: gi|18659233|gb|BM500228.1|BM500228
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|211174646|gb|FL281696.1|FL281696
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|211176315|gb|FL281701.1|FL281701
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAADATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|211176317|gb|FL281703.1|FL281703
EST:     CTCCTCAAGAACTTGATTATCTTATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATA
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATA
EST: gi|20301115|gb|BQ164058.1|BQ164058
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|67039619|gb|CO465874.1|CO465874
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCCTGA-CATATAAAATTCGACCATGGTTATACCTCTAA
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCC-TGAACATATAAAATTCGACCATGGTTATACCTCTAA
EST: gi|20299937|gb|BQ162880.1|BQ162880
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|67021475|gb|CO450224.1|CO450224
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGGAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|211176314|gb|FL281700.1|FL281700
EST:     CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
EST: gi|211174647|gb|FL281697.1|FL281697
EST:     CTCCTCAAGAACTTGATTATCT-ATTTGTGGTCGCTGTGAACTTTGGGAG                         CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG
genomic: CTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAG

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), 48 (downstream exon)
Score: 164

GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 74

GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 68

GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttt ... catcatgcagCCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTTGACATATCATCACTGCAAATATTTTCTCCTCAAGAACTTGATTATCTGATTTGTGGTCGCTGTGAACTTTGGGAGgtattgcttttgtggtcattcttgatgttgtacttcctctgtcccagaatgataagcatagtttgtataggaaaaagtcaaatttagaattttatttccc

- - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaaa