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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttcacagttctttaattcttccgttcagaagtcttggcaccacttggttccaacactagcttttcacctcacgtttcttctgcaccatgcag

Basic information

species Zea mays
transcript GRMZM2G129155_T01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 19
AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttcacagttctttaattcttccgttcagaagt-cttggcaccacttggttccaacactagcttttcacctcacgtttcttctgcaccatgcag
||| || || || |  ||| |||||| |||||| ||||| |||||||||||||||| ||| |||||||| |  |||||||||||||| ||||| ||||| ||| |||||  |||  ||  | || | |  || |  ||   ||   ||   ||| | | |||| ||  ||   |  |   |    |    ||   | |||
AGACGACCTCTTTGCGGACATGCTCAGAGAACCCGATGAAATAACCATAAAGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttgtcagaacta-agttttccattttaatagcatttcatactgattgat-ctaacattaaatt---atttattggccttgtgacatgcttcag
















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|5847452|gb|AW000531.1|AW000531
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|211024339|gb|FL478389.1|FL478389
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|33100316|gb|CF060276.1|CF060276
EST:     TCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: TCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|5895668|gb|AW036914.1|AW036914
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|88758145|gb|DY542286.1|DY542286
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|33097482|gb|CF057442.1|CF057442
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|32828402|gb|CD968080.1|CD968080
EST:     AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: AGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
EST: gi|71448926|gb|DR829976.1|DR829976
EST:     ACAAGCTTACAAA                         ACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC
genomic: ACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATAC

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), 48 (downstream exon)
Score: 71

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


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

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 109

AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttc ... caccatgcagACTTTGGACGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGATACTCCCTGGATTCTGATGCGATTGGTCTGCCAAGGGCCCATGGGCTTTCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGATCTTTTGGAAGACTTGCTCAAAGAACCTGATGAGATAACCATAAAGAGGAAGCAGATACGTGAAAATCTCAAGGTCCTTCAACAAGCTTACAAAgtacgttttcacagttctttaattcttccgttcagaagtcttggcaccacttggttccaacactagcttttcacctcacgtttcttctgcaccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT