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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtactgtgtgctactttaaagatacattgtgttgttgctccaattctcttacatacctttgttcatgtgaccaaataatgcag

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g56850.2 (Oryza sativa), 5'ss of exon 6
GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtaga---gtactgtgtgctactttaaag----atacattgtgttgttgctccaattctcttaca--tacctttgttcatgtgaccaa-ataatgcag
||  | ||||||||||| ||||||||||| || ||||||||||| ||||| || ||||||||||| |||||||||||       ||| |  | | | || | |    ||| |||||  |||   ||||| | ||| | |  | | ||||||||||||      ||| |||||
GAGTTAGCTATTACTTCAGATGAGGCCTTAAGTTTGGAGGAGCTACCAAAACGTGCTGTAATCCTTGGTGGCGGgtatgtctacactctagggtgcatttatgtactatatattgttatgtcattccaactatctcagacttgcatttgttcatgtggtggctatattgcag
















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|211287654|gb|FL367858.1|FL367858
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|149099075|gb|EE185096.2|EE185096
EST:     GCCTTGAGCTTGGAGGAGCTTTCAAAGCGCGCTGTATTCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGA
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGA
EST: gi|148994377|gb|EE034060.2|EE034060
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211462691|gb|FL336836.1|FL336836
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211123447|gb|FL321141.1|FL321141
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|149014256|gb|EE043820.2|EE043820
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATC
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATC
EST: gi|24934176|gb|CA452394.1|CA452394
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGNCTGTTGAATTTGCTCCTATCTGGAGGGGGATGGGTGCTGAAG
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTG-CTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAG
EST: gi|211135367|gb|FL349825.1|FL349825
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211426648|gb|FL071976.1|FL071976
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|148937231|gb|EC881413.2|EC881413
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211396212|gb|FL320934.1|FL320934
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|149077608|gb|EE166308.2|EE166308
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGGGGCGG                         ATATATTGCTGTTGAATTTGCTTC
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTC
EST: gi|211460047|gb|FL333663.1|FL333663
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|76293305|gb|DV032873.1|DV032873
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|149108741|gb|EE292941.2|EE292941
EST:     CCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGNTA-TCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTG
genomic: CCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTG-TAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTG
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211540781|gb|FL336428.1|FL336428
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|32938226|gb|CF043045.1|CF043045
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|31611973|gb|CD568595.1|CD568595
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAAT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAAT
EST: gi|76012767|gb|DT939937.1|DT939937
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|211318389|gb|FL341246.1|FL341246
EST:     AATCCTGGGTGGCGG                         ATATATTGCTGTTGAAYTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: AATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
EST: gi|24934516|gb|CA452734.1|CA452734
EST:     GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGG                         ATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT
genomic: GCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGT

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: 455

GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4118

GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3350

GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 718

GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtact ... aataatgcagATATATTGCTGTTGAATTTGCTTCTATCTGGAGGGGGATGGGTGCTGAAGTAGATTTGTTTTATCGAAGAGATCTTCCTCTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGGCTATTACTTCTGATGAGGCCTTGAGCTTGGAGGAGCTTCCAAAGCGCGCTGTAATCCTGGGTGGCGGgtagagtactgtgtgctactttaaagatacattgtgttgttgctccaattctcttacatacctttgttcatgtgaccaaataatgcag

- - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - -  GAGCTT