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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaactcattatatgttttcag

Basic information

species Zea mays
transcript GRMZM2G009030_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 5
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaactcattatatgttttcag
||||||||||||||||||||| ||||||||||||||||| ||||| ||||| ||||| || |||||||||||| ||||| |||| ||||||||||| ||||||  |||||  ||  | |   |      || ||| |  |    |  || ||      || | |||||||| | ||  |     | || ||||  |||
TTCAAAAGCTGCTGGTTGGGGCGTGATGGTCAGCCACAGGAGTGGGGAAACGGAAGATAATTTCATCGCAGATCTGGCTGTTGGTTTAGCAAGTGGTCAGgtag-ggactatcaccatcagaaatct--taactgtggtaccaaaattctacgaacgctcatcagatgatcctaacacactcattcatgtgttg-cag

upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 5'ss of exon 5
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaactcattatatgttttcag
 ||||||||||| || |||||||||||||| || ||||| ||||| || || || || ||||||||||||||| |  || |||| |||||||| || |||||| |  |   ||   ||  ||  |||  |  ||     | ||| |    | |   ||   ||   |                               
CTCAAAAGCTGCAGGCTGGGGTGTGATGGTTAGTCACAGGAGTGGCGAGACAGAGGATAACTTCATCGCAGATCTCTCTGTTGGTTTAGCAAGCGGACAGgtacatcaaatcctctaaacctgtctgtattactctc-tagtgtttgcttatcattctctgttttgtag-----------------------------

upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 5'ss of exon 5
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaactcattatatgttttcag----
 || |||||||| || ||||||||||||||||| ||| | ||||||||||| ||||| |||||||| || ||| |  || | ||||| |||||||| |||||      ||  |||     ||   ||||          ||| | | | |  ||   |    | | || |    |   | |   |||| | || |||     
CTCTAAAGCTGCAGGATGGGGTGTGATGGTCAGTCACCGGAGTGGTGAAACAGAAGATAACTTCATAGCTGATCTTTCTGTGGGCTTGGCAAGTGGACAGgtt-----ctatcagctgaactccttgagctct------attatgtgttctgctttttattgttgctgcttgaaattaaccattttatgttttgtcatatag

upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S76_97V6.1 (Physcomitrella patens), 5'ss of exon 4
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgta-------------aaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttag-atgatcatgacggaactca-----ttatatgttttcag------------------------------
||| || || || ||||||||||| |||||||||||| ||||||| || || |||||||  || || || ||  |  || | ||| | || || || ||||||             |||     |||  ||       || ||| ||       |   ||| || |||  |    ||    | |  |     | || |     ||   ||||||                                 
TTCCAAGGCAGCCGGTTGGGGTGTTATGGTCAGCCACCGAAGTGGAGAGACTGAAGACACTTTTATTGCTGACCTCTCTGTGGGCCTTGCGAGCGGACAGgtattccgatttcttcaagtttcaccatgaattacccttgtgtaactagtgtccttgttatgcaactgtttctgctattgcgtttttcgatcagcttagttgctttcttgtttttgcctgaggatctgacactaatttcctactcag

upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ26490 (Selaginella moellendorffii), 5'ss of exon 6
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaact-cattatatgttttcag
||||||||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||  || || || ||  ||||| ||||  | || ||||| ||||||         |         |  |  |    |   | |     | |   | ||| |  ||| |||  |  |  |     | |||  | |  ||||||
TTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCGAGGACACATTTATTGCGGACCTGGCTGTTGGACTCGCTAGTGGACAGgtaccaattcttcgactttttaaagtttgcttgtagaatagctctttttgtcttgattcgcttcgatccttttctcatcgtttcatgttctcgtttcag

upper sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ26799 (Selaginella moellendorffii), 5'ss of exon 5
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaact-cattatatgttttcag
||||||||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||  || || || ||  ||||| ||||  | || ||||| ||||||         |         |  |  |    |   | |     | |   | ||| |   || |||  |  |  |     | |||  | |  ||||||
TTCAAAAGCTGCTGGATGGGGTGTTATGGTGAGCCACAGAAGTGGAGAGACCGAGGACACATTTATTGCGGACCTGGCTGTTGGACTCGCTAGTGGACAGgtaccaattcttcgactttttaaagtttgcttgtagaatagctctttttgtcttgattcgtttcgatccttttctcatcgtttcatgttctcgtttcag

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|32866424|gb|CF006106.1|CF006106
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|76290554|gb|DV030122.1|DV030122
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|22819501|gb|BU499591.1|BU499591
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAG
EST: gi|76011516|gb|DT938686.1|DT938686
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|166632552|gb|EG255936.1|EG255936
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACTGGGGCTCCATGCCG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCG
EST: gi|33102792|gb|CF062752.1|CF062752
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|149004756|gb|EE039253.2|EE039253
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|76290528|gb|DV030096.1|DV030096
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|7135894|gb|AW498320.1|AW498320
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
EST: gi|87156544|gb|DY401333.1|DY401333
EST:     CCGAAGACAACTTCATCGCAGATTTGGCTGTTGGCTTAGCAAGTGGGCAG                         ATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG
genomic: CCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG

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), 45 (downstream exon)
Score: 83

TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 79

TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 523

TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggact ... atgttttcagATTAAAACCGGGGCTCCATGCCGCAGCGAGAGGCTGGCCAAATACAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAAAAGCTGCTGGTTGGGGTGTGATGGTCAGCCACAGAAGTGGTGAAACCGAAGACAACTTCATCGCAGATTTGGCTATTGGCTTAGCAAGTGGGCAGgtaaaggactgccagaaacgctagctgagtagctgagacattgtatatccacctgacttccttagatgatcatgacggaactcattatatgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG