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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattttctcccagtcccagcaacttcaatgatatcacctggttggtctcttattcaactgctccgttctgtttggtttcttcccaaattatggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 8
acattttctcccagtcccagcaacttcaatgatatcacctggttggtctcttattcaactgctccgttctgt-ttggtttcttcccaaattatggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
                         |   ||  ||     | | |   | | ||     |  | | | |    ||| |    | | |   |  |  | |||||||||||||||||||| |||||||| ||||| || || || |||||||||||||||||||||||||||||||| || || |||||||| ||||||||||
------------------------gttggtgtgatttgaagctagaattatcatattgatattgcttacaacattgctaaaatactattgtccgtctacagGCTGTGATCAATGCAAACATAATTGCTCCTCTAGTACATCTGCTGCAAACTGCTGAATTTGACATCAAGAAAGAGGCTGCGTGGGCAATCTCAAATGCCA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
------acattttctcccagtcccagcaacttcaatgatatca----cctggttggtctcttattcaactgctccgttc-tgtttggtttcttcccaaattatggt-tgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
      | |||||             |   |||||  ||||      | ||  ||  || ||     |  | ||   |    |||    |  |        ||| | || ||||||| ||  |||| || || ||| ||||| ||||    || ||    || || ||||||||||||||||| ||||| || ||||| |||||||||||||
gtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S230_50V6.1 (Physcomitrella patens), 3'ss of exon 7
------------acattttct-cccagtcccagcaacttcaatgatatcacctggttggtctcttattca----actgctccgttctg--tttggtt--tcttcccaaattat----ggttg-------cagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
            ||  |   |   || |||| |    ||  |   |         ||   ||| | ||||    ||||    ||  |   |||  ||  | | |   |||  |    |||||       ||||| |||||  | || || || ||| |||| || ||     | ||    |||||||| ||||||||||||||||||||||| ||||| ||||| |||||||
gtattaatttccactctccttattcaatccctgttgattggagattgcttttattttccactcctgttcactgcactgtgtagtcatacttttaattgatgtactataatcgttttcggttgtctactacagGCCGTGATTGACGCGAACATTATTCCACCGCTTGTATCTTTGCTCGCCACTGCTGAGTTTGACATCAAGAAAGAAGCAGCTTGGGCTATTTCGAATGCCA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------acattttctcccagtccca--gcaacttcaatg-atatcac-ctggttggtctcttattcaactgctccgttctg---------tttggtttc-----ttcccaaatt--------atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
                ||| | | |      | |   | |  | |||| | | ||| |   |  |||| |    |||  |     ||| |         | |||| ||     ||  ||||||        |   ||||||||||| ||  |||| || || ||| ||||||||||    || ||     | |||||||| |||||||||||||| |||||||||||  | || ||||| |
gttggattcgaatcttcatctgcccatgcctcgactacgagctaaatgcacagcacacccttctgtctgtggagcaataggagttttcagaaagtaatctctggtatcagatgttaacaaatttgttcgggaaatttgcagGCTGTAATTGATGCCAACATTATTCCACCTCTGGTATCCCTGCTTGCGTCAGCTGAATTCGACATCAAGAAAGAGGCAGCCTGGGCGGTGTCCAATGCAA

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|6564217|gb|AW231839.1|AW231839
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|213179381|gb|FM182985.1|FM182985
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|60338095|gb|DN205068.1|DN205068
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|6587581|gb|AW244899.1|AW244899
EST:     CATGCTGGACGATCTCAAACATCACAGCTGG-AACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|211452349|gb|FL292614.1|FL292614
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|211452353|gb|FL292618.1|FL292618
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCT-G-SHRACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
EST: gi|33097597|gb|CF057557.1|CF057557
EST:     CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAG                         GCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT
genomic: CATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACT

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: 643

CCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 626

CCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 445

CCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 532

CCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACATCACAGCTGGTAACAAGGAGCAGATTCAGgtttgtgtgc ... atggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctcttattcaactgctccgttctgtttggtttcttcccaaattatggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA
                                        aaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acattttctcccagtcccagcaacttcaatgatatcacctggttggtctcttattcaactgctccgttctgtttggtttcttcccaaattatggttgcagGCTGTGATCAATGCAAATATAATTGCACCTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - -cagcaac
- - - - - - - - - - - - - - - - - -cacctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctcc