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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaagcttacctttacctgtgtttaatttcattgatagaaacactttgcccttattattaaagtttttttaaaccaaagtgtgttctttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA

Basic information

species Zea mays
transcript GRMZM2G027756_T01
intron # 16
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|37388207|gb|CF631310.1|CF631310
EST:     AAATAGTCAAGAGGTTCAAAG                         TGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: AAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
EST: gi|71773326|gb|DR971232.1|DR971232
EST:     GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAG                         CGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
EST: gi|32931563|gb|CF036375.1|CF036375
EST:     GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAG                         TGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
EST: gi|76282536|gb|DV022104.1|DV022104
EST:     GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAG                         CGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
EST: gi|32930056|gb|CF034868.1|CF034868
EST:     GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAG                         TGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
EST: gi|33091466|gb|CF051460.1|CF051460
EST:     GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAG                         TGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG
genomic: GGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGG

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), 49 (downstream exon)
Score: 213

TAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

TAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 74

TAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 216

TAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTGGAGTAAATAGTCAAGAGGTTCAAAGgtatttcaag ... tttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactttgcccttattattaaagtttttttaaaccaaagtgtgttctttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA
                                          ttctttatcct  CT-rich tract
          ttattattaaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcaagcttacctttacctgtgtttaatttcattgatagaaacactttgcccttattattaaagtttttttaaaccaaagtgtgttctttatcctagCGAGGATGTGGACACGCAGAAAGGTCACAAATTACGGCAATTACCTGATGGGCAGTCAGCCTCTCGTGCTAGTTCTGTAGCTTCACCTGCAGTCTCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG