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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatagcagaagtgtgcaataaatgtgagcttagaatgaccttagtatgaagtaagtgggtattctgcaagttacaaaaaactgttttaagataaa...

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 5'ss of exon 12
CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatagcagaagtgtgcaataaatgtgagcttagaatgaccttag-tatgaagtaagtgggtattctgcaagttacaaaaaac-tgttttaagataaa-
 ||||||||||| || || || || ||||||||||||| |||||||||||||||||||||||||||||||||   ||||||||| ||| ||  | || ||||| ||  |||| |||| | | ||| |  |||||| | ||||| || |   ||||| ||     ||  ||  | ||||| ||    | |   ||  | |    
GATTCTGAGTTTGGCAGCAGGTGTAGAATCAAATACAACCCACCCGCTTGGAAAAGCCATCATGGAAGCTGCTCAGGCTGCCAATTGCCTCTATCTGCAGgtagtcgcagcaaaagtatactatatacctgagct-aaaatgatctgaaacatgaattacaaaagt--tcgtctagttaaaatttgcgtaccttctgttttta
















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|32929758|gb|CF034570.1|CF034570
EST:     GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|78104271|gb|DV522689.1|DV522689
EST:     GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|211170367|gb|FL103276.1|FL103276
EST:     GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|13125965|gb|BG316640.1|BG316640
EST:     GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: GAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|32929848|gb|CF034660.1|CF034660
EST:     AGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: AGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|32929738|gb|CF034550.1|CF034550
EST:     GCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: GCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
EST: gi|32929733|gb|CF034545.1|CF034545
EST:     TGCAGGGGCTGCCAACTGCGTCATTATGAAG                         GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC
genomic: TGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACC

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), 49 (downstream exon)
Score: 168

CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 128

CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 114

CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatag ... gttgtcacagGCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTCTGAGTTTTGCTGCTGGAGTGGAATCAAATACAAACCACCCGCTTGGAAAAGCCATCATGGAAGCTGCAGGGGCTGCCAACTGCGTCATTATGAAGgtaatcatagcagaagtgtgcaataaatgtgagcttagaatgaccttagtatgaagtaagtgggtattctgcaagttacaaaaaactgttttaagataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG