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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatcttgacagcaatatgtgataaacttcgatatcttattgaactcagttaccagtattaaccgtgccaaatggtcatgattcag

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 7
AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatcttgacagcaatatgtgataaacttcgatatcttattgaactcagttaccagtattaaccgtgccaaatggtcatgattcag
|| |||| |||||||| || || || |||||||||||| | || |||||||||||||| |||  |||||| ||||| ||||| ||||||||| ||||||||||||| | |   || || |||||| ||| ||  |  | || ||  |  || || ||  |  | |        ||        ||||||
AGATCGGAATAGTTCTCGATTTTAATTGGTATGAACCTCTAACTAACTCAACTGAAGACCAAGCAGCAGCTCAAAGAGCCAGAGACTTCCATGTTGGTTGgtaagaccatagaagtaacatgtgacaaagttaaaggttttgtttgatacaatttccgatgctgataaaaatcaactacttcaattcag
















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|32832647|gb|CD972325.1|CD972325
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|67013218|gb|CO441967.1|CO441967
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAACGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|78075435|gb|DV503869.1|DV503869
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|149081710|gb|EE170863.2|EE170863
EST:     ACTGAAGATCAAAAAGCAGCGCAGAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|149081712|gb|EE170865.2|EE170865
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAA
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAA
EST: gi|60351674|gb|DN218647.1|DN218647
EST:     AAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: AAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|149013746|gb|EE043205.2|EE043205
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|60340042|gb|DN207015.1|DN207015
EST:     ACTGAAGAT-AAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|60394083|gb|DN226953.1|DN226953
EST:     ACTGAAGA-CAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|149014535|gb|EE044169.2|EE044169
EST:     ACTGAAGATCAAAAAGCAGCGCANAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|40336432|gb|CK370502.1|CK370502
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|32834810|gb|CD974488.1|CD974488
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
EST: gi|20507721|gb|BQ279747.1|BQ279747
EST:     ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTG                         GTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT
genomic: ACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACAT

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: 226

AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACATTGTGAAAGACCGGCTACCAAGTTTCACACCTGAACAGGCCAAGCTAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACATTGTGAAAGACCGGCTACCAAGTTTCACACCTGAACAGGCCAAGCTAGTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 64

AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACATTGTGAAAGACCGGCTACCAAGTTTCACACCTGAACAGGCCAAGCTAGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 182

AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatctt ... catgattcagGTTTCTTGATCCATTAATAAATGGGCAATATCCAAAGATAATGCAAGACATTGTGAAAGACCGGCTACCAAGTTTCACACCTGAACAGGCCAAGCTAGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGGACTTCCATATTGGTTGgtaagatcttgacagcaatatgtgataaacttcgatatcttattgaactcagttaccagtattaaccgtgccaaatggtcatgattcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG