Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcgtttcagaattccatccacagtctgtagtaatgaggatgtatgaagtgaactgaaacgctcgtcgatctggtgcttcgtcgcacaatttgccgcag

Basic information

species Zea mays
transcript GRMZM5G848603_T03
intron # 7
splice site 5'
intron type U2

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|76924733|gb|DV170107.1|DV170107
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|71771831|gb|DR969768.1|DR969768
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|71421242|gb|DR805356.1|DR805356
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCTTCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|149005842|gb|EE040132.2|EE040132
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTTCTCCA
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTT-CTCCA
EST: gi|211455215|gb|FL443682.1|FL443682
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|50331305|gb|CO526431.1|CO526431
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|71306517|gb|DR789416.1|DR789416
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|78110730|gb|DV529128.1|DV529128
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|149107875|gb|EE292236.2|EE292236
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|31353484|gb|CD437841.1|CD437841
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|76014004|gb|DT941174.1|DT941174
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
EST: gi|71315893|gb|DR794634.1|DR794634
EST:     GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATAT                         AAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC
genomic: GGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAAC

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), 41 (downstream exon)
Score: 33

GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 20

GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcg ... tttgccgcagAAAATCGATAAGGTGCTCAAGAGGTTCGGCAGCAACATCATCTTCTCCAACGGAATGCGAGACCCATGGAGCCGTGGCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGTCCGCCTTCAGCTACGACGACAGGTCCGACGAGTGTTTCCAGAGCTGGGGGGTTCGGCCGAGGCCGCACTGGATCACCACTGAGTACGGTGGATATgtaggtgtcgtttcagaattccatccacagtctgtagtaatgaggatgtatgaagtgaactgaaacgctcgtcgatctggtgcttcgtcgcacaatttgccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA