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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttatcctgaatgtgtagtcaagtataattatgaaaccatatgataatgaagcagtttctggggattatcttatcttatctatctcatggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA

Basic information

species Zea mays
transcript GRMZM2G038588_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038588_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12570.1 (Oryza sativa), 3'ss of exon 6
------catt-ttatcctgaatgtgtagtcaagtataattatgaaaccatatgataatgaagcagtttctggggattatcttatcttatctatctcatggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA
       |||  | |   |  | ||| | |||||   || |||||     |||| ||||||   ||  |||  ||||   | || | || | |||       ||||||||||||| ||||||||| | ||||||||||   |||  ||| |||||||||||||||||||||||||||||||||| |||||||| |  |||||| |||
cgaaactattgctgttaggtttatgttgacaagtgctatcatgaataagcatga-aatgaaatggtc-ctgaagattggatcatttgatttgtcta-----ctgcagGAGAAACTATGGAAGATGCTAAAAGATGCAGCAAAAAATAAGCCCAACATTGATGTTGTAAAACTTCATAAATCAGAAGGTGTTGTTCCGAGAAATCCAA
















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|71323423|gb|DR798362.1|DR798362
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|149010086|gb|EE041893.2|EE041893
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|31405753|gb|CD484485.1|CD484485
EST:     CCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: CCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|50338323|gb|CO533449.1|CO533449
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|71763129|gb|DR961066.1|DR961066
EST:     AATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: AATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|71324526|gb|DR798964.1|DR798964
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|86471476|gb|DY237846.1|DY237846
EST:     ACGCAATTGAAACCTTCAAGGCCAAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: ACGCAATTGAAACCTTCAAGGCC-AATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|211074603|gb|FK960576.1|FK960576
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAWGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|93014406|gb|EB639926.1|EB639926
EST:     TCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|110518920|gb|EE023507.1|EE023507
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|71448836|gb|DR829886.1|DR829886
EST:     CAAACGCA-TTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTG
genomic: CAA-CGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTG
EST: gi|149073620|gb|EE161922.2|EE161922
EST:     GCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGGCAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: GCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|78075700|gb|DV504134.1|DV504134
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|71324528|gb|DR798965.1|DR798965
EST:     TCAACGCAATTGAAACCTTCA-GGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGT-GAAAGATGCAGTTCAAAGCAAG
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAG
EST: gi|149034778|gb|EE155078.2|EE155078
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|60401015|gb|DN233822.1|DN233822
EST:     TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: TCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|78081105|gb|DV509517.1|DV509517
EST:     ACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: ACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|211013387|gb|FL466952.1|FL466952
EST:     CAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: CAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|78122373|gb|DV540757.1|DV540757
EST:     AATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTTTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: AATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
EST: gi|86471665|gb|DY238035.1|DY238035
EST:     AAGGCCAATGTAGTACTGGTACTGGGACAG                         GAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT
genomic: AAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATT

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), 49 (downstream exon)
Score: 249

TTACTTCTCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 91

TTACTTCTCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

TTACTTCTCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 86

TTACTTCTCAACGCAATTGAAACCTTCAAGGCCAATGTAGTACTGGTACTGGGACAGgcaagttctg ... tggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataatgaagcagtttctggggattatcttatcttatctatctcatggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA
                      attatcttatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttatcctgaatgtgtagtcaagtataattatgaaaccatatgataatgaagcagtttctggggattatcttatcttatctatctcatggcttgcagGAGAAACTCTGGAAGATGTTGAAAGATGCAGTTCAAAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAA

- - - - -ctgaatg
- - - - - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - -gaagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggg