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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaaagggataaagtgcagtgtagtttgtttaccattagaattcaatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g32610.4 (Oryza sativa), 3'ss of exon 12
----aacaa-agggataaagtgcagtgtagtttgtttaccattagaattcaatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT-------------------------------
    | ||  |||  ||   | |  | || | |  ||  || | |  |||  |    |   || |  |    |||   ||  | | | || |    || |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||                               
tatgatcattaggattatctttctttctaatataattggcagttg--ttccctatttaatcttatctccaactaacaacaaatttcccctaca---atgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACTGTAAGTTCATATTACCGTTACTTTTATTTGT

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 12
----aacaaagggataaagtg-cagtgtagtttgtttaccattagaattcaatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT
    | ||   |||| |  |  |  | || | |  ||  || | |  |||  |    |   || |  |    |||   ||  | | | || |    || |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
tatgatcattaggattatctttctttctaatataattggcagttg--ttccctatttaatcttatctccaactaacaacaaatttcccctaca---atgctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTTTGTCTTCCAAGACTGCAGCAGGGACT
















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|20802940|gb|BQ293990.1|BQ293990
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     TTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: TTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     GGGATCTTGAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC

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), 48 (downstream exon)
Score: 71

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT


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

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT
                              tgtcttcacttctctt  CT-rich tract
                                          tcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaaagggataaagtgcagtgtagtttgtttaccattagaattcaatgaccatctttctacctgtgtaatgtcatgtcttcacttctcttattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG