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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgttatgtgcatagcattacactataattgatctggactctcgaattgagattgaaagtgtaaataaggggaaaaaaggttgattgaagtaactaatgatcctgtgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g44070.1 (Oryza sativa), 3'ss of exon 9
gtacttgttatgtgcatagcattacactataattgatctggactctcgaattgagattgaaagtgtaaataaggggaaaaaaggttgattgaagtaactaatgatcctgtgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT
||| |||| |  ||  | ||||       | |  | | ||        || |  |     || | ||||  |      |||| ||| |  ||  | | |  | ||  | | |||||||||||||||||||||||||||| | ||  |||||||| |||||||| |||  |   ||||||| ||| ||||||| ||||||||||||||| || || ||||
gtatttgtcagttgttttgcat------gttaacggtatga-----taaagttggtccacaaatataaactat-----aaaatgttcaaggacatgatt--ttattttatattttccagCTTCAACAAAGTGTGGCCCCCAAAAGGGCTGATCCGCAAGGTCTATGGCGAGGATGTAGGATGAATCATGCCTCCTGTAATAGCAACCAACTGCAATTTT
















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|148953387|gb|EE152881.2|EE152881
EST:     ACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: ACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|91056470|gb|EB166888.1|EB166888
EST:     ATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: ATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|211266712|gb|FL294975.1|FL294975
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|101383816|gb|EB813963.1|EB813963
EST:     GAACACTGCCTATGACGTGTGGCAG                         GTTCAACAAAGTGTGGCCCCTAGAACAGGTGATCCCCAAGGTCTTTGGTCA
genomic: GAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|67018103|gb|CO446852.1|CO446852
EST:     CCATTCGAACTCCAACTTTTGTTTTGAACACTGCCTACGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|91051274|gb|EB161692.1|EB161692
EST:     TTGTTTTGAACACCTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: TTGTTTTGAACA-CTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|31356908|gb|CD441265.1|CD441265
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|78025651|gb|DV494038.1|DV494038
EST:     CTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|149009226|gb|EE153857.2|EE153857
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|149101141|gb|EE187249.2|EE187249
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|76932739|gb|DV173141.1|DV173141
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|32837541|gb|CD977219.1|CD977219
EST:     CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
EST: gi|60401537|gb|DN234344.1|DN234344
EST:     CTGCCTATGACGTGTGGCAG                         CTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA
genomic: CTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 221

TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 257

TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 385

TGCTTTTTCCCCCAGAATGTGTTGCCAACCATCCGAACCCCAACTTTTGTTTTGAACACTGCCTATGACGTGTGGCAGgtacttgtta ... tgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaataaggggaaaaaaggttgattgaagtaactaatgatcctgtgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT
                               aactaat  putative branch site (score: 385)
                                             tgttttcc  putative PPT
                              taactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgttatgtgcatagcattacactataattgatctggactctcgaattgagattgaaagtgtaaataaggggaaaaaaggttgattgaagtaactaatgatcctgtgttttccagCTTCAACAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC