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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttgctatctggtagctagtagtattttgccagttctttgttggtgctatcgattttctagatgacgttgtcctatgtttattgcttggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC

Basic information

species Zea mays
transcript GRMZM2G138907_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138907_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 3'ss of exon 3
gtcagtttgctatctggtagctagtagtattttgccagttctttgttggtgctatcgattttctagatgacgttgtcctatgtttattgcttggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC
|| || |   ||||||||| ||||||  | || |  |     |||||  ||            |||| |         |||  | |||| |||||  || |||||||||||||||||||||||||||||||||||| || ||||| |||||||| |  || |||||||||||||| ||||| || || || |||||||||||
gtaagctacatatctggtacctagtaaaacttgggta-----ttgttactg------------tagaag--------ttataataattgattggctctacagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGAAAAGCTCTAACCTCCACTGACCGTTTTGAGATGTGGGGAGATGGTCTTCAGACTAGATCCTTCAC
















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|71318270|gb|DR795899.1|DR795899
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|76282745|gb|DV022313.1|DV022313
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCTTTCGGCACATGAAAAG                         GTGAAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|148945328|gb|EC890545.2|EC890545
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|148931952|gb|EC875193.2|EC875193
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAANGCGCCTGCTGCTTTCTG
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTG
EST: gi|116813381|gb|EC855825.1|EC855825
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|32866083|gb|CF005765.1|CF005765
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|60399538|gb|DN232349.1|DN232349
EST:     CACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|76282746|gb|DV022314.1|DV022314
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAAGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
EST: gi|78119627|gb|DV538011.1|DV538011
EST:     CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAG                         GTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA
genomic: CCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCA

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), 46 (downstream exon)
Score: 39

GCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 303

GCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

GCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACAACATATATGGTCCCTTCGGCACATGGAAAGgtcagtttgc ... ggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgctatcgattttctagatgacgttgtcctatgtttattgcttggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC
                               tatgtttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttgctatctggtagctagtagtattttgccagttctttgttggtgctatcgattttctagatgacgttgtcctatgtttattgcttggcaatatagGTGGAAGGGAGAAGGCGCCTGCTGCTTTCTGCAGGAAGGCTCTGACCTCCACAGGGCGCTTTGAGATGTGGGGTGATGGCCTGCAAACCAGATCCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG