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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttctatatccatattttgttctgtacattatcaaacggtgaggccctaagttgttttgtatgatcttttcgtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT

Basic information

species Zea mays
transcript GRMZM2G108849_T01
intron # 9
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|6020622|gb|AW065655.1|AW065655
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|67013050|gb|CO441799.1|CO441799
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|33100201|gb|CF060161.1|CF060161
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|37383229|gb|CF628607.1|CF628607
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|32924024|gb|CF028836.1|CF028836
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGCCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|5922310|gb|AW055599.1|AW055599
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|60347914|gb|DN214887.1|DN214887
EST:     CCGTCAAGTTGATTGGATGGGAAACCAGTGATGCTGGAGAGGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|33103672|gb|CF063632.1|CF063632
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|6095470|gb|AW120137.1|AW120137
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|32941550|gb|CF046369.1|CF046369
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|5005885|gb|AI711947.1|AI711947
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|37385964|gb|CF630150.1|CF630150
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|161586543|gb|EY957605.1|EY957605
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGG                         CTTCTGGCAAATCAGTGGAA
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAA
EST: gi|37376423|gb|CF624736.1|CF624736
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTCATGCTGGAGAGGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|32941251|gb|CF046070.1|CF046070
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|24934282|gb|CA452500.1|CA452500
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
EST: gi|5361062|gb|AI795677.1|AI795677
EST:     CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAAGATTACTGG                         CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
genomic: CCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT

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), 36 (downstream exon)
Score: 201

CAAATCTGGAGTGTACAAGCACATCACCGGTGGCATTATGGGTGGCCATGCCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 750

CAAATCTGGAGTGTACAAGCACATCACCGGTGGCATTATGGGTGGCCATGCCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 1086

CAAATCTGGAGTGTACAAGCACATCACCGGTGGCATTATGGGTGGCCATGCCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 291

CAAATCTGGAGTGTACAAGCACATCACCGGTGGCATTATGGGTGGCCATGCCGTCAAGTTGATTGGATGGGGAACCAGTGATGCTGGAGAGGATTACTGGgtatgttgtt ... gtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatcaaacggtgaggccctaagttgttttgtatgatcttttcgtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT
                                      tcttttcgtctttgc  CT-rich tract
                            ttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgttctatatccatattttgttctgtacattatcaaacggtgaggccctaagttgttttgtatgatcttttcgtctttgcagCTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA