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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaagctccattcagaatgggtgcgtacatgttcctctccctccaaggaaacgctaatcatcgtttgtgttggtgttatgttgcgcag

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T03 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 24
TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaagctccattcagaatgggtgcgtacatgttcctctccctccaaggaaacgctaatcatcgtttgtgttggtgttatgttgcgcag
|||||||||| |||||||| |||||||| || || ||||| ||||| || || || || ||||| |||||||||||  | |||||| ||||||| |||||||||  | ||||| ||| | |||  |  | |   |     | ||||    | |||||   || | |  |  ||    || ||| |||  ||||
TTGGTCAGGCTGGAAGGCCCAAGACAATTACTGGTTTCCAAACACATTCGACACCCGTATTGCTTGCAGCAGGGGAACGGGCTGAATTAGCAACCGAAAAgtaataagagctcaattaacaatatgc-catttctacaagtttcccc---atgaaacctaaaacctgatccgtt---gttttacgttttgcag
















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|32867559|gb|CF007241.1|CF007241
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATTCCACCGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|60347371|gb|DN214344.1|DN214344
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|6031296|gb|AW076153.1|AW076153
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTGGCAACTGAAAA                         ATACATTCCACTGACCCCAGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|38687344|gb|CK144375.1|CK144375
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTC
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTC
EST: gi|5847123|gb|AW000202.1|AW000202
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTGGCAACTGAAAA                         ATACATTCCACTGACCCCAGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|211100370|gb|FL070848.1|FL070848
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|211334276|gb|FL040639.1|FL040639
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTGGCAACTGAAAT                         ATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATCCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
EST: gi|18175836|gb|BM351006.1|BM351006
EST:     ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA
genomic: ACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAA

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: 305

TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAACCCAGAGTACCACGAGGAGTGAAGACCCAGATAGCATATTGGTGTTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAACCCAGAGTACCACGAGGAGTGAAGACCCAGATAGCATATTGGTGTTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAACCCAGAGTACCACGAGGAGTGAAGACCCAGATAGCATATTGGTGTTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaag ... tgttgcgcagATACATTCCACTGACCCCGGTACTAGAGGGCTTTGTGATTCTGAAGAAGAACCCAGAGTACCACGAGGAGTGAAGACCCAGATAGCATATTGGTGTTTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTCAGGCAGGAAGGCCGAAGACAATCACCGGCTTCCAGACACACTCCACGCCGGTCTTGCTCGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaaagaaagctccattcagaatgggtgcgtacatgttcctctccctccaaggaaacgctaatcatcgtttgtgttggtgttatgttgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA