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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattctttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgagcattctgatgtggtgttgtgatacag

Basic information

species Zea mays
transcript GRMZM5G868168_T04
intron # 5
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|50324151|gb|CO519277.1|CO519277
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|149004790|gb|EE039293.2|EE039293
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|19057652|gb|BM736319.1|BM736319
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAACGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|149078033|gb|EE166771.2|EE166771
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|211065956|gb|FK946601.1|FK946601
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|211065957|gb|FK946602.1|FK946602
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTTCAAAGTGCTGCACTTTTTTGATTCTCTCACAGTTCGTGAAAATG
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTT-CAAAGTGCTGCACTTTTT-GATTCTCTCACAGTTCGTGAAAATG
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAACGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|149080766|gb|EE169831.2|EE169831
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCNAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|91048130|gb|EB158548.1|EB158548
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|19436793|gb|BM953203.1|BM953203
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATGGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAACGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT
EST: gi|31356046|gb|CD440403.1|CD440403
EST:     GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTG                         GTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAACGTT
genomic: GGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTT

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), 48 (downstream exon)
Score: 29

GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 88

GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattc ... tgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGATGTAATCATTTGTGGAAAGAAAAGGCATGGTTTAGTTAGCGATGAGGATATAGAGGGTCTCCGCATTGGTTTGgtacatattctttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgagcattctgatgtggtgttgtgatacag

- - - - - - - - - - - - - - - - - - - - - - - - GAGGAT