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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtacattgtcaattgaagctgaggattttttttatatgttgagtaggatttcatttcagttgttatcattctaagtagttgttcggtgtttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA

Basic information

species Zea mays
transcript GRMZM5G824405_T01
intron # 2
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|211455006|gb|FK979208.1|FK979208
EST:     GGCGGCCACCGCNGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211452890|gb|FK979205.1|FK979205
EST:     GGCGGCCACCG-CGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211452892|gb|FK979207.1|FK979207
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211455013|gb|FK979215.1|FK979215
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211452887|gb|FK979202.1|FK979202
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211452889|gb|FK979204.1|FK979204
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211455010|gb|FK979212.1|FK979212
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211455012|gb|FK979214.1|FK979214
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211452886|gb|FK979201.1|FK979201
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211455009|gb|FK979211.1|FK979211
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCACAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAA
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCA-AGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAA
EST: gi|211452891|gb|FK979206.1|FK979206
EST:     GGCGGCCACCG-CGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
EST: gi|211455008|gb|FK979210.1|FK979210
EST:     GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACG                         AATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT
genomic: GGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAAT

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: 41 (upstream exon), 37 (downstream exon)
Score: 28

CTGCCTTTGGAGCGGGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

CTGCCTTTGGAGCGGGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 26

CTGCCTTTGGAGCGGGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

CTGCCTTTGGAGCGGGCGGCCACCGCCGTGTGGGAGTTCAGCTGCGTCGTGCCTTCGCAGCACGgtaagttggt ... tttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggatttcatttcagttgttatcattctaagtagttgttcggtgtttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA
                                             tttttact  CT-rich tract
                                             tttttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtacattgtcaattgaagctgaggattttttttatatgttgagtaggatttcatttcagttgttatcattctaagtagttgttcggtgtttttactagAATCGCTGGATTTCAAGTTTGTTTTGAAGCGAAAAGGTGATAATCCTCAATACATTATTGAGGAGGGACCTAACCGACCATTGGGTTGCCAGAGAAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - gaagctg
- - - - - - - - - - - - - - - - - - -atgttga