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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatctaatttagatcggccgtaagatgggacctttgtttgcagctctgcaaacctctgcaatttagttgacatttagcttctctcgacccctctcaacttcttgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G167356_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167356_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12850.1 (Oryza sativa), 5'ss of exon 4
GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatct-aatttagatcggccgtaagatgggacctttgtttgcagctctgcaaacctctgcaa--------tttagttgacatttagcttctctcgacccctctcaacttcttgtttatgcag
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||  ||||||||| ||||| |  |||||| |  || | ||| |   ||  | | |||||        ||| | |     || ||||||||  | |   || ||||| || ||| | |||
GCATACTAAGATGCCTCGTGGATTTGGATTTGTTACATTTTCCGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAGCACGTTATAGATGGAAGAACGgtaggacatcttgatttagatcagccgttacgtgggacttcagtctacagttg-acactcttttgcaaagtcgcactttgggtttatcttggcttctctttatcttgcttaactt-ttatttgttcag
















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|9255383|gb|BE345851.1|BE345851
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|148946214|gb|EC891510.2|EC891510
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|211107234|gb|FL370789.1|FL370789
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCCGAGG-AAGAGATGAATACCNAAGATGG
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCC-GAGGGAAGAGATGAATACCAAAGATGG
EST: gi|148932748|gb|EE285380.2|EE285380
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|148939672|gb|EC884331.2|EC884331
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|148935082|gb|EC879124.2|EC879124
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|78116552|gb|DV534939.1|DV534939
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGA-GAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|71439287|gb|DR820337.1|DR820337
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|78108850|gb|DV527267.1|DV527267
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|71427627|gb|DR808677.1|DR808677
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
EST: gi|78076701|gb|DV505135.1|DV505135
EST:     CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACG                         GTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC
genomic: CTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGC

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: 613

GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGCCCTAAGACAAGAAAGATCTTCATCGGTGGGCTACCTGCATCTCTTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 474

GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGCCCTAAGACAAGAAAGATCTTCATCGGTGGGCTACCTGCATCTCTTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGCCCTAAGACAAGAAAGATCTTCATCGGTGGGCTACCTGCATCTCTTACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 559

GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatc ... gtttatgcagGTGGAAGTCAAGAGGACAGTTCCGAGGGAAGAGATGAATACCAAAGATGGCCCTAAGACAAGAAAGATCTTCATCGGTGGGCTACCTGCATCTCTTACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATACTAAGATGCCTCGTGGATTTGGATTCGTTACATTTTCTGATCCATCTGTTATAGACAAGGTTTTGGAGGATGAACACGTTATAGATGGCAGAACGgtagggcatctaatttagatcggccgtaagatgggacctttgtttgcagctctgcaaacctctgcaatttagttgacatttagcttctctcgacccctctcaacttcttgtttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG