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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttgacaacctaaaccaccttcaattgtgttcataatgtttccactatcataaacgcttttcctcaattgcaattactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 14
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|211354438|gb|FK991815.1|FK991815
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211094713|gb|FL034685.1|FL034685
EST:     AAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCCATAGAG                         GATGTCACATCACAAGGNGATAAATGGAAGACGTCTACATTCAACTCAAA
genomic: AAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTC-ATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAA-TG-AAGACGTCTACATTCAACTCAAA
EST: gi|211097187|gb|FL034699.1|FL034699
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211354445|gb|FK991822.1|FK991822
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|86465874|gb|DY232247.1|DY232247
EST:     AAAGTTTATCTCCAGATCCTAAAAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACTTTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211094718|gb|FL034690.1|FL034690
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATT
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATT
EST: gi|211354440|gb|FK991817.1|FK991817
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCNCATCNCAAGGNGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211354441|gb|FK991818.1|FK991818
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|9794356|gb|BE552664.1|BE552664
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211097189|gb|FL034701.1|FL034701
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211094725|gb|FL034697.1|FL034697
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211354443|gb|FK991820.1|FK991820
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
EST: gi|211354442|gb|FK991819.1|FK991819
EST:     AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAG                         GATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA
genomic: AAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTA

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: 401

CACTGAGCTGCCAATCCGCCGATGGACTCAGGATTACAAAGATTTTCTCGAAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 26

CACTGAGCTGCCAATCCGCCGATGGACTCAGGATTACAAAGATTTTCTCGAAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 24

CACTGAGCTGCCAATCCGCCGATGGACTCAGGATTACAAAGATTTTCTCGAAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 22

CACTGAGCTGCCAATCCGCCGATGGACTCAGGATTACAAAGATTTTCTCGAAAGTTTAGCTCCAGATCCTAAGAACAAGGACAAAGTAACATTCATAGAGgtagttgaca ... tactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataatgtttccactatcataaacgcttttcctcaattgcaattactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT
                                            ttacttt  CT-rich tract
                                          aattacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttgacaacctaaaccaccttcaattgtgttcataatgtttccactatcataaacgcttttcctcaattgcaattactttacagGATGTCACATCACAAGGTGATAATGAAGACGTCTACATTCAACTCAAATTAAGTGAGGCAAATGTGAATGTAGCTAAGGAAGAAGGACTAGTGAAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT