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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG

Basic information

species Zea mays
transcript GRMZM5G866758_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
--atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
      || | |        ||          | | |  | | ||||| ||    |    | | |  || | ||||  | || |  |  | | |  ||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtact-atgtaatttgatcattatgt-gcctcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 7
atgcaacgttccttgca---taatgagctttgctagcagttatttgtaagat--caatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
    |    |   ||||   || | |   | |  |  |||| | ||||   |  || |  |  |||  |  || ||| | || |  | | | |||  | |   |||||||  | |  ||  ||   |||||||| |||||||||||||||| ||| ||| | ||||| ||||| |||||||| || |||||
----acttctagctgcaaattagttactatagtcattagttttgtgtatacttgcagttgaatacaaatcaatatat-tgttatattttccttttcctatgccagTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 5
atgcaacgttccttgcataatgagctttgctagcagttat-ttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
|      | | ||   ||  | |   | |  |  | || | |  ||   ||| |  |  |||  |  || ||| | || |  | | | |||  | |   |||||||  | |  ||  ||   |||||||| |||||||||||||||| ||| ||| | ||||||||||| |||||||| || |||||
acttctagctgctattattgttactatagtcattatttttgtcttactttcagttgaatacaaataaatatat-tgttatattttccttttcctatgccagTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
atgcaacgttccttgcataatgagctttgctagcag--ttatttgtaagatcaatgcatgac--agttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
   ||     | |     |||||   |||     |   | | |   || |   |    | |   ||| | ||||    | |||   ||  ||    ||||| |||||||  | | |||| | | |||||| || || |||||||| |||||||| || || ||||||||||||||||| ||||| |||||
---cattacacgtcagcaaatgaaacttgtggttaagataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctca-atgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 8
atgcaacgttccttgcataatgagctttgctagcagttatttg--taagatcaa--tgcatgacagttt-tatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
       |||| |||   ||  |  | |      |   | |     || || |   |   ||  | | |  ||| ||||||  |||| ||    || | |  ||||||||||| || ||| ||||||| || || || ||||| ||||||||||| ||| | || || || || ||||||||||| |||||
----ttagttctttgagaaaataaatatatagatacagaatcaatcaatattaccttctttgttaatatacattaatgtctattgctcttgtgctttt-tgctagTTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 7
-atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtctt---agTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
   | ||  | |||| | |    ||       |    |  | ||     |||||||    |  ||||  ||   |  |  | ||| |  |||   ||||   |||||||  | | |||||||| ||||||||| ||||||||||||||   ||| ||| ||||||| || || ||||||||||| |||||
ccagtaat-taccttacctgtcaagaaacaa-attcatgttctgggttctcaatgc-catccattttccttgctttctaagatat-caatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGA---TGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG

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|211193824|gb|FL472434.1|FL472434
EST:     GCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|31909501|gb|CD650950.1|CD650950
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|18661821|gb|BM501596.1|BM501596
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCA-GTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|93281704|gb|EB673968.1|EB673968
EST:     ATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: ATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|76921549|gb|DV168617.1|DV168617
EST:     ATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: ATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|18450558|gb|BM428836.1|BM428836
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|76284259|gb|DV023827.1|DV023827
EST:     TAGAGGAAAACCCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: TAGAGGAAAA-CCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|18654813|gb|BM499618.1|BM499618
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|87152006|gb|DY396795.1|DY396795
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|211292808|gb|FL187022.1|FL187022
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|32864390|gb|CF004072.1|CF004072
EST:     AAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
genomic: AAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT
EST: gi|22490195|gb|BU050118.1|BU050118
EST:     GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG                         TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCATTTATAATGGT
genomic: GTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGT

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: 205

GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 352

GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 312

GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 280

GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAGgtattttttc ... tgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
                                      ttccttttgtgtctt  CT-rich tract
                 ttttatttatgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - -tccttgc
- - - - - - - - - - - - - -tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga