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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttacatgccttcttttgctttcaattcatgttggaattttagtggatattgacaaggtttgttgttagcttactatcacgtttggtttttttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 16
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|76280738|gb|DV020306.1|DV020306
EST:     GAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
EST: gi|211316883|gb|FL253819.1|FL253819
EST:     GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
EST: gi|93014018|gb|EB639538.1|EB639538
EST:     GAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGC
genomic: GAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACA-CCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGC
EST: gi|76929334|gb|DV171965.1|DV171965
EST:     GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
EST: gi|211316876|gb|FL253812.1|FL253812
EST:     GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
EST: gi|211316881|gb|FL253817.1|FL253817
EST:     GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
EST: gi|211316879|gb|FL253815.1|FL253815
EST:     GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAG                         CCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA
genomic: GTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 371

AAAAATACTTGCCAACACTGATGGACAACGCTTGCTTAGGATGCTTGAGAGTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 82

AAAAATACTTGCCAACACTGATGGACAACGCTTGCTTAGGATGCTTGAGAGTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

AAAAATACTTGCCAACACTGATGGACAACGCTTGCTTAGGATGCTTGAGAGTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

AAAAATACTTGCCAACACTGATGGACAACGCTTGCTTAGGATGCTTGAGAGTAGAGCATTTGAGGGCTCTAGAGGACCTCCTCAACAAATAAACACCAAGgtagtgatat ... tttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattgacaaggtttgttgttagcttactatcacgtttggtttttttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG
                                         tttttttatt  CT-rich tract
                                    tttggtttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttacatgccttcttttgctttcaattcatgttggaattttagtggatattgacaaggtttgttgttagcttactatcacgtttggtttttttattgcagCCTCCAATTGTCGCCCTTGGTCCTGTTTCAAATGTCAGCAGTCCTATAGCAGTAAATGCCGAGCGACCTGATCGGATCTTGCCTGCAGTGTCGACAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- tacatgc
- - - - - - - - tgctttc
- - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt