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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttcttggcattgaaatgctaatcttgaactgtgtggtacatttcaatcatctcgagttttttttttttttgaaattttggtgcctctattccttt...

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 5
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|71421501|gb|DR805467.1|DR805467
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         T-----CCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|32837204|gb|CD976882.1|CD976882
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|9953455|gb|BE640038.1|BE640038
EST:     TTGACTGAAGCTCAACAGGAAGTGCATACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGNCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         T-----CCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|71326005|gb|DR799685.1|DR799685
EST:     TGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGTCA-G                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGAT
genomic: TGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATG-CAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGAT
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         T-----CCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|50325446|gb|CO520572.1|CO520572
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|44682243|gb|CK787291.1|CK787291
EST:     TGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTTCCTGATGCAAG                         TATAGTCCAAAAAGCCTCTAGTGTCATGGAAGTATTGAGG
genomic: TGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTT-CCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGG
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|211276223|gb|FL230638.1|FL230638
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAG                         TATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA
genomic: TTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAA

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: 353

CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 204

CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttctt ... gttttttcagTATAGTCCAGAAAGCCTCTAGTGTCATGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTCCCAGAAACGAGAACAGAACCAAATAATGAAAGTTTATCGACCCGTTTGACTGAAGCTCAACAGGAAGTGCACACTCAGCCTGTTCCTGATGCAAGgtactttcttggcattgaaatgctaatcttgaactgtgtggtacatttcaatcatctcgagttttttttttttttgaaattttggtgcctctattccttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA