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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgcactcttttgcagcaaccttttgttttttgaacccaatgtactccagtatacaaaaatattgtatggtgttataccaatgaattcttatttttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT

Basic information

species Zea mays
transcript GRMZM2G011136_T01
intron # 6
splice site 3'
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|6020843|gb|AW065771.1|AW065771
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
EST: gi|71767791|gb|DR965728.1|DR965728
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
EST: gi|71445898|gb|DR826948.1|DR826948
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
EST: gi|5325032|gb|AI783223.1|AI783223
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
EST: gi|32931583|gb|CF036395.1|CF036395
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGATTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
EST: gi|5846844|gb|AI999927.1|AI999927
EST:     GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAG                         GATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC
genomic: GTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTAC

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: 47 (upstream exon), 48 (downstream exon)
Score: 59

GTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 180

GTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

GTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGCTCAGGGTTACCAGgtatctgcac ... tttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatacaaaaatattgtatggtgttataccaatgaattcttatttttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT
                                     ttcttatttttact  CT-rich tract
                               aatgaattcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgcactcttttgcagcaaccttttgttttttgaacccaatgtactccagtatacaaaaatattgtatggtgttataccaatgaattcttatttttactacagGATTGACCGGTTATTTTCTAAGAAACAACATTTGAAGCCAAAGAATGGTACGAAGAAGACTGATGAAATTAATGAAGATGAAGAAGATCCAGAATTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG