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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgacacctgctttggatagcaagaatgtctctaatgatagatttctttgatgcttaggttcttgtcgatcccctctaacccatctctattcttta...

Basic information

species Zea mays
transcript GRMZM2G173321_T02
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|149051909|gb|EE156042.2|EE156042
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|18180982|gb|BM382192.1|BM382192
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|78074656|gb|DV503090.1|DV503090
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|78093455|gb|DV521829.1|DV521829
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|21626184|gb|BQ621105.1|BQ621105
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|78544304|gb|DV621802.1|DV621802
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|211213891|gb|FL469119.1|FL469119
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|211111375|gb|FK984521.1|FK984521
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGCTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|60345741|gb|DN212714.1|DN212714
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|78093454|gb|DV521828.1|DV521828
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|71333334|gb|DR803728.1|DR803728
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|60397540|gb|DN230356.1|DN230356
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAAAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACT
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACT
EST: gi|93281470|gb|EB673734.1|EB673734
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|20507481|gb|BQ279651.1|BQ279651
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|71333335|gb|DR803729.1|DR803729
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|78544746|gb|DV622244.1|DV622244
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
EST: gi|213170597|gb|FM195452.1|FM195452
EST:     TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAG                         GTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC
genomic: TTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAAC

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: 32 (upstream exon), 48 (downstream exon)
Score: 112

GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAACTAATAGCTTGTAATGTGGTGTTTGGAGCACAG


Block sizes: 32 (upstream exon), 39 (downstream exon)
Score: 31

GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAACTAATAGCTTGTAATGTGGTGTTTGGAGCACAG


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 31

GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAACTAATAGCTTGTAATGTGGTGTTTGGAGCACAG


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 25

GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgaca ... aatggtgcagGTAATCATAATTAGAGCAAGTTCTTACTATGAAAGTGAGGACTGATGAAACTAATAGCTTGTAATGTGGTGTTTGGAGCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGGCCTCAGCGCTGGATGGAGAGGGTTCGCTATCCAGCACAAGCTGGTTGATGGAGATTGCTTGGTCTTCCAGCTGACTGAGAGAACAAAGTTCAAGgtgagtgacacctgctttggatagcaagaatgtctctaatgatagatttctttgatgcttaggttcttgtcgatcccctctaacccatctctattcttta

- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA