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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caactattatgattttgtttcttaactttatcttttatggaatgtgactgcatctgtgatgaatgacctcaactgtctataacctccattcaattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 12
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|211094279|gb|FL470654.1|FL470654
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|5607818|gb|AI901485.1|AI901485
EST:     CAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|111991228|gb|EE332430.1|EE332430
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|16919952|gb|BM074437.1|BM074437
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|37377887|gb|CF625588.1|CF625588
EST:     CTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|24764480|gb|CA399644.1|CA399644
EST:     CTCCAGTAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|32907008|gb|CF011821.1|CF011821
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|60396317|gb|DN229186.1|DN229186
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|62550542|gb|DN830962.1|DN830962
EST:     CTCCAGCAAGAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAAGGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|32919364|gb|CF024176.1|CF024176
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|37401565|gb|CF638149.1|CF638149
EST:     CTCCAGTAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|116823588|gb|EC867128.1|EC867128
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|13515771|gb|BG518047.1|BG518047
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|33095213|gb|CF055207.1|CF055207
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|149072974|gb|EE161235.2|EE161235
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|50336101|gb|CO531227.1|CO531227
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|32921823|gb|CF026635.1|CF026635
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
EST: gi|78120607|gb|DV538991.1|DV538991
EST:     CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG                         GTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT
genomic: CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATT

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: 45 (upstream exon), 48 (downstream exon)
Score: 615

CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 328

CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 333

CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 333

CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGgtactttact ... caattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgcatctgtgatgaatgacctcaactgtctataacctccattcaattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG
                               ctataac  putative branch site (score: 333)
                                     cctccattc  CT-rich tract
                                          attcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caactattatgattttgtttcttaactttatcttttatggaatgtgactgcatctgtgatgaatgacctcaactgtctataacctccattcaattggcagGTTCTATGGATCACGCGGAAGGGACGAGAGCAGATCAAACAATGATGGATTCCGTGCTAGGAGCAGAAGTCCTGGCAAGCCTGTGGAAGTTTCCAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - -ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaatg