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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgctctcttctttgctaacttgacgcttttaatatcagtcagatatatgctttgatataaattgcagcaccagaacatcaaatgaatagtcaaatgtgatgcttactcttttcaaatatcatgcgatgttcttttttttcattaacattttttctgccaaaatgattctcccag

Basic information

species Zea mays
transcript GRMZM2G078576_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078576_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 17
ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgctctctt-ctttgctaacttgacgcttttaatatcagtcagatatatgctttgatataaattgcagcaccagaacatcaaatgaatagtcaaatgtgatgcttactcttttcaaatatcatgcgatgttcttttttttcattaacattttttctgccaaaatgattctcccag
|||||| ||||||||  | || |||||||| |||||||||||||||||  |||| ||||||| ||||||  | |  ||   |  | |  | | |  |   |     |  | ||||  | ||||    || | ||||   |||  |   ||   | |||                                                                              
ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttactctctggcctcactttttataagactctcacttgctttcctcacttccttttttttaaaaaa-agaatcaga---tcaggttggtatgtatatgc-----------------------------------------------------------------------------
















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|211398218|gb|FL061021.1|FL061021
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|71438781|gb|DR819831.1|DR819831
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|87155515|gb|DY400304.1|DY400304
EST:     CCTTCAATCCCAACGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|78111274|gb|DV529671.1|DV529671
EST:     CCTTCAATCCCAGCGCCATAAATCTTTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|71759659|gb|DR957596.1|DR957596
EST:     CCTTCAATCCCAGCGCCATAAATCTTTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|24766669|gb|CA401816.1|CA401816
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCCCCTTGAA                         GATGCCCCAGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCTGAACCAGA
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCC-GAACCAGA
EST: gi|22472877|gb|BU037357.1|BU037357
EST:     CCTTCAATCCCAACGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|84980715|gb|DW531064.1|DW531064
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCAGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|37377989|gb|CF625644.1|CF625644
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCAGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|211145552|gb|FL475586.1|FL475586
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|149083574|gb|EE172908.2|EE172908
EST:     CCTTCAATCCCAGCGCCATAAATTTTTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|37376751|gb|CF624930.1|CF624930
EST:     CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCAGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|148945634|gb|EC890893.2|EC890893
EST:     CCTTCAATCCCAGCGCCATAAATTTCTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
EST: gi|93282383|gb|EB674647.1|EB674647
EST:     CCTTCAATCCCAGCCCCATAAATTTTTTCCCTGTGGAGATTCACCTTGAA                         GATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG
genomic: CCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAG

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: 43 (upstream exon), 49 (downstream exon)
Score: 60

ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAGTTCTGACAAGGAACATAAAGGCATATTTTTGTTCCATTGTGGCAAAGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 36

ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAGTTCTGACAAGGAACATAAAGGCATATTTTTGTTCCATTGTGGCAAAGAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 35

ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAGTTCTGACAAGGAACATAAAGGCATATTTTTGTTCCATTGTGGCAAAGAG


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

ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgct ... attctcccagGATGCACCGGCCGGTGAACAAAAGGTTTAGGAAGAATGGTCCGAACCAGAGTTCTGACAAGGAACATAAAGGCATATTTTTGTTCCATTGTGGCAAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTCCTTCAATCCCAGCGCCATAAATCTCTTCCCTGTGGAGATTCACCTTGAAgtaagttgctctcttctttgctaacttgacgcttttaatatcagtcagatatatgctttgatataaattgcagcaccagaacatcaaatgaatagtcaaatgtgatgcttactcttttcaaatatcatgcgatgttcttttttttcattaacattttttctgccaaaatgattctcccag

- - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAT