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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctttgctgcatgtcactatttactctacttttgttttcaatcacttcattgatgggacctactgtaactaacttagagtgtacaatttgttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 4
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|149090120|gb|EE179418.2|EE179418
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211516878|gb|FK974814.1|FK974814
EST:     ACTGCGGATTCATCTTCCGAGGGCCGCAGACTCC-GTTAATCCAAAATTG                         GTTTTATCTTCCA-TAGGATACAATGGACGA
genomic: ACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAA-TTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGA
EST: gi|149089319|gb|EE178541.2|EE178541
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211514522|gb|FK974800.1|FK974800
EST:     CTGCGGATTCAATCTTCCGAGGGCCGCAGACTCCAGTTAATCCCAAATTG                         GTTTTATCTTCCAATAGGA
genomic: CTGCGGATTCA-TCTTCCGAGGGCCGCAGACTCCAGTTAATCC-AAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGA
EST: gi|211153843|gb|FK974844.1|FK974844
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGT
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGT
EST: gi|149008951|gb|EE041170.2|EE041170
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     GGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: GGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|29168004|gb|CB411264.1|CB411264
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATA
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATA
EST: gi|211153845|gb|FK974846.1|FK974846
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGG
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGG
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|149104775|gb|EE290237.2|EE290237
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCNATAGGATACAATGGACGAGCATCATCTATAG
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAG
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     CGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: CGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|86466218|gb|DY232591.1|DY232591
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGAACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211514526|gb|FK974804.1|FK974804
EST:     ACTGCGGATTCATCTTCCGAGGGCCGCAGACTCC-GTTAATCCCAAATTG                         GTTTTATCTTCCAATAGGATAC
genomic: ACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCC-AAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATAC
EST: gi|149094603|gb|EE180134.2|EE180134
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|101398071|gb|EB820910.1|EB820910
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211516883|gb|FK974819.1|FK974819
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTTATCCAAATTG                         GTTTTATCTTCCAATAGGGATACA-TGGACGAGCATCATCTATAGTTGTGT
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGG-ATACAATGGACGAGCATCATCTATAGTTGTGT
EST: gi|93015898|gb|EB641418.1|EB641418
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATTGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211512177|gb|FK974795.1|FK974795
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCCAATTG                         GGTTTTATCTTCCA
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagG-TTTTATCTTCCA
EST: gi|31350712|gb|CD435069.1|CD435069
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|31355275|gb|CD439632.1|CD439632
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|71424525|gb|DR806344.1|DR806344
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|148983250|gb|EE029217.2|EE029217
EST:     ACTGCGGATTCATCTTTCC-AGGGCCGCAGACTCCAGTTAATCCCAATTG                         GTTTTATCTTCC
genomic: ACTGCGGATTCATCTT-CCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCC
EST: gi|149106513|gb|EE188405.2|EE188405
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|89253028|gb|DY624814.1|DY624814
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTC
EST: gi|211516880|gb|FK974816.1|FK974816
EST:     AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTG                         GTTTTATCTTCCAATAGGATACAATGG
genomic: AACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGG

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: 269

TCACGGTTGGAGGTTACACAGATTTCTTTTGTTCTGTGCACCATGCAAGGAACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 234

TCACGGTTGGAGGTTACACAGATTTCTTTTGTTCTGTGCACCATGCAAGGAACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 142

TCACGGTTGGAGGTTACACAGATTTCTTTTGTTCTGTGCACCATGCAAGGAACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 500

TCACGGTTGGAGGTTACACAGATTTCTTTTGTTCTGTGCACCATGCAAGGAACTGCGGATTCATCTTCCGAGGGCCGCAGACTCCAGTTAATCCAAATTGgtaatgtgtt ... gttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattgatgggacctactgtaactaacttagagtgtacaatttgttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG
                      aactaac  putative branch site (score: 500)
                                          tttgttc  putative PPT
                                     tacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctttgctgcatgtcactatttactctacttttgttttcaatcacttcattgatgggacctactgtaactaacttagagtgtacaatttgttcattcagGTTTTATCTTCCAATAGGATACAATGGACGAGCATCATCTATAGTTGTGTCTGGAACCGATGTAATTAGGCCCAG

- - ttgctgc
- - - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - -attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctactg