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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtaactaccgacagatcagcagccactacactaccggactcgccttcgtacgtgttcgttctgacgcgcgcggcgtgcgttcccctgcaccatgcatgtttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC

Basic information

species Zea mays
transcript GRMZM2G122172_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122172_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g39230.1 (Oryza sativa), 3'ss of exon 3
gcaagtaactaccgacagatcagcagccactacactaccggac-tcgccttcgtacgtgttcgttctgacgcgcgcggcgtgcgttcccctgcaccatgcatgtttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC
                                        ||  ||        |  |||   ||   ||  |  |   |  || |  | | || | |   | ||| || ||||||  |||||| ||||| || ||||| || || || |||||| ||||||||||| |||||||||||||||| ||    || ||||| ||||||||||| |
------------------------------------gtaagatatcatacattcagctgtcaattagcacatgaacattgatcggtttcttacaactttttttttttttgcagGTGGCTTTCACGGGATCTACTGAGGTTGGACGGCTTATAATGGAGGCCTCCGCGAAGAGCAACCTGAAGCCGGTGGCACTCGAGCTCGGCGGCAAGTCGC
















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|76936946|gb|DV174974.1|DV174974
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGC
EST: gi|148942564|gb|EC887583.2|EC887583
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|76020436|gb|DT947606.1|DT947606
EST:     TGGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|78083932|gb|DV512325.1|DV512325
EST:     TGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|149087182|gb|EE176719.2|EE176719
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|78074898|gb|DV503332.1|DV503332
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|148959027|gb|EC905199.2|EC905199
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|148948769|gb|EC894170.2|EC894170
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|78091392|gb|DV519766.1|DV519766
EST:     TCGGCCCGACGGCAAAAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|148993480|gb|EE033799.2|EE033799
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
EST: gi|71426117|gb|DR807167.1|DR807167
EST:     TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATG                         GTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC
genomic: TCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCC

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 3 RNA-Seq libraries.


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 1

GCAGGGGTCCCAGACGGCGTGATCAACGTCGTGCCAGGCTTCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC


Block sizes: 39 (upstream exon), 24 (downstream exon)
Score: 4

GCAGGGGTCCCAGACGGCGTGATCAACGTCGTGCCAGGCTTCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC


Block sizes: 39 (upstream exon), 40 (downstream exon)
Score: 5

GCAGGGGTCCCAGACGGCGTGATCAACGTCGTGCCAGGCTTCGGCCCGACGGCAGGAGCCGCGCTGGCGTCTCACATGGACGTTGACATGgcaagtaact ... tttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgttctgacgcgcgcggcgtgcgttcccctgcaccatgcatgtttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC
     ttctgac  putative branch site (score: 5)
                                             tttgtttc  putative PPT
                                             tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtaactaccgacagatcagcagccactacactaccggactcgccttcgtacgtgttcgttctgacgcgcgcggcgtgcgttcccctgcaccatgcatgtttgtttcagGTGAGTTTCACCGGATCCACGGAGGTCGGGCGCCTCATAATGAAGGCCTCCGCGGAGAGCAACCTGAAGCCCGTCTACCTGGAGCTGGGCGGCAAGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT