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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttggtgtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG

Basic information

species Zea mays
transcript GRMZM2G140689_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 7
gtatgtttggtgtttagtgctcatagctcaggacatgcttct-aatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG---------------------
                  |  |||     || || |    || || || |||  ||| ||    |  |||||  |  ||||    | | | |||| | | ||||||||||||||||||||||||| |||||  | || ||||| ||||||||||| |||||||| || ||||| || ||||                     
------------------gtacatttacaagcacttaagcctgaacattgcagcagccttgctct-tatgctaattacatgtttgtgttctcaatttggtagGTTCCTGGTGTTCCAATCATGTATATCACTCGGCACAGGTACTCGATAGAACGACTCCCTGAAGCTACAATCGGAGGAGGTAATGTATTTTGTGCTGGTG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g06410.2 (Oryza sativa), 3'ss of exon 7
gtatgtttggtgtttagtgctcatagctcaggacatgcttct-aatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG
                  |  |||     || || |    || || || |||  ||| ||    |  |||||  |  ||||    | | | |||| | | ||||||||||||||||||||||||| |||||  | || ||||| ||||||||||| |||||||| || ||||| || ||||
------------------gtacatttacaagcacttaagcctgaacattgcagcagccttgctct-tatgctaattacatgtttgtgttctcaatttggtagGTTCCTGGTGTTCCAATCATGTATATCACTCGGCACAGGTACTCGATAGAACGACTCCCTGAAGCTACAATCGGAGGAG
















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|19769624|gb|BQ034345.1|BQ034345
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|89252677|gb|DY624463.1|DY624463
EST:     ATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCGTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: ATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19770099|gb|BQ034820.1|BQ034820
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|211091999|gb|FL476412.1|FL476412
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19436894|gb|BM953304.1|BM953304
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|37383195|gb|CF628588.1|CF628588
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|166471289|gb|EG109651.1|EG109651
EST:     CTTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGA
genomic: C-TACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGA
EST: gi|19057702|gb|BM736369.1|BM736369
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|78083854|gb|DV512247.1|DV512247
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19436893|gb|BM953303.1|BM953303
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGNGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|50330326|gb|CO525452.1|CO525452
EST:     TGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: TGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|5649962|gb|AI920322.1|AI920322
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
EST: gi|19057549|gb|BM736231.1|BM736231
EST:     GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAG                         GTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA
genomic: GCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAA

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: 134

CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 51

CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 77

CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 93

CACAAATGCTACATAGTTGCTACTTGTGATAGAGATTTGAAAAGGAGGATAAGAAAGgtatgtttgg ... aatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG
                                      tttcccca  CT-rich tract
          tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttggtgtttagtgctcatagctcaggacatgcttctaatatcgcaaaagctttttcatgcatgcttgtaccatgggcatttccccaatcttgcagGTTCCTGGTGTTCCAATCATGTACATCACAAGACATAGGTATTCGATAGAACGGCTCCCTGAGGCCACAATTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG