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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaataaaggaattccatatcttttagtttctatacatctctaccttcatgtgatgatgacttggtttagggtatactgattattatctttgtctatgtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 6
gtgagtaataaaggaattccatatcttttagtttctatacatctctaccttcatgtgatgatgacttggtttagggtatactgattattatctttgtc----tatgtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG
|||||||| |||  | |||  | |||||||||||      |    ||  ||   ||     |   ||  |||   ||     |    |||| ||||||    | |||   | |||||||||||||| ||||||| ||||| ||||| |||||||| |||||||||||||||||  |||||||||||||||||||||||||||| ||||| || ||
gtgagtaacaaatta-ttctttctcttttagtttacgactactcatatttt---gtcgaagttttttcttttcatgttcgtcgtcacttatttttgtcttcctctgttgctgcagCTAAAGAAAGAATCTATCCTGTTGCTGATGCTACTACCTTTTTTACTGATATGCACTATATCCTTCGTGTGTTGGCTGCTGGGGATATTCGAACTGTATG
















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|71772853|gb|DR970776.1|DR970776
EST:     CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
genomic: CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
EST: gi|32929645|gb|CF034457.1|CF034457
EST:     TACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGTCGATGCAACTACCTTCTTTACTGATA
genomic: TACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
EST: gi|19058010|gb|BM736677.1|BM736677
EST:     CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
genomic: CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
EST: gi|50336750|gb|CO531876.1|CO531876
EST:     CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
genomic: CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
EST: gi|22490387|gb|BU050310.1|BU050310
EST:     CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
genomic: CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
EST: gi|87153046|gb|DY397835.1|DY397835
EST:     CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT                         CTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA
genomic: CCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATA

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: 48 (upstream exon), 48 (downstream exon)
Score: 88

CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG


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

CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 70

CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATTgtgagtaata ... gtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatgacttggtttagggtatactgattattatctttgtctatgtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG
                      tactgat  putative branch site (score: 70)
                    tatactgattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaataaaggaattccatatcttttagtttctatacatctctaccttcatgtgatgatgacttggtttagggtatactgattattatctttgtctatgtcattacagCTAAAGAAAGACTCTATCCAGTTGCCGATGCAACTACCTTCTTTACTGATATGCACTACGTCCTTCGTGTGTTGGCTGCTGGGGATATCCGAACCGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT