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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttccttgaactgtatacaaactgacatcaattcatattctgatatctgacagcatgtttcacttgccag

Basic information

species Zea mays
transcript GRMZM2G074687_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 7
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttccttga--actgtatacaaactgacatcaatt-catatt-ctgatatctgaca---gcatgtttcacttgccag
||||||||||||||||| |||||||||||||| |||||||| || |||||||| ||||| || ||||| ||||||||||| |||||||| ||    |   || |    || | |   |||   | || || |||||| ||| | |||||||    ||||||||  || ||||
CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacatgtttctttttccag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgt--atggcagttcct--tg-aactgtatacaaactgacat-caattcatattctgatatctgacagcatgtttcacttgccag-----------------------
||||| || |||||||| |||||||||||||| |||||  ||||||||||| ||||||| || ||||| || ||||||||   | ||||   ||| | ||  |  || || | | ||  |  ||| || | |   ||    | || | ||  |     |||  ||| | |                        
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAGgtttgtggaaatttttattgtaaatttgtaatatttgaaatacgacatattccattatgtttggtaatgaattt-gctttctaactttgcatgctacatatttgcag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgt--atggcagttccttg---aactgtatacaaactgacatcaattcatattctgatat-ctgacagcatgtttcacttgccag----------------------
||||| || |||||||| |||||||||||||| |||||  ||||||||||| ||||||| || ||||| || ||||||||   ||||||   ||| | ||  ||    || | | ||  |  ||| || |   |||||||   |||  |   |     |||   ||   |                       
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaaatttgttttgtaaatttgtaatatatgaaat-atgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttc----cttgaactgtatacaaactgacatcaattcatattctgatatctgacagcatgtttcacttgccag---
||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| || ||||| ||   |||||| |  ||||| ||   |||     ||||||| |  ||   |      ||| || || |||     ||| || |  ||||  | |   | |   
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggt-tgttgtattgttctgtag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttcct----tgaactgtatacaaactgacatcaa-----ttcatattctgatatctgacagcatgtttcacttgccag
||||||||||||||||| || ||||||||||| ||||||||||| || || |||||||| || ||||  ||   |||||| |  ||||| || || || ||      ||  ||||  | |      ||||     ||| |  ||| |   ||| ||  || |||   | |    
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtcaatttctattccaaaaagtatctatatcctggtcaacgtttttcttcctctcaaggctgtcaa-atatttttgtag----

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgt--atggcagttccttgaactgtatacaaactgacatcaattca-tattctgatatctgacagcatgtttcacttgccag------
||||| || |||||||| |||||||||||||||||||| || || |||||| ||||||| || ||||| ||||||||||| | ||||||   |||||     ||    |   |  ||||  |  | | ||   |  |   | |  || ||  ||   || ||  |         
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaac--atttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 7
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttccttgaactgtatacaaactgacatcaattcat---attctgatatctgacagcatgtttcact-tgccag------------
||||| || |||||||| ||||||||||||||||||||  | || || ||  | ||||| || ||||| ||||||||||| |  |||||        ||  |||| ||| ||  |  | | || |  | ||   ||| ||  |  |||| |     || | | | |  |            
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACACCTCCAACAATAGCTAACCCTGAGTACAAGGGACCATGGAAGCCCAAGgt--------tcgctgaaatgtttattagttaagatgatgttatggaattttggaagttgacggttcacttaattgttcttgaaccattggcag

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|40337074|gb|CK371144.1|CK371144
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|211279487|gb|FL438453.1|FL438453
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|32846103|gb|CD985784.1|CD985784
EST:     CTGCCCCCACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|58029459|gb|CX724886.1|CX724886
EST:     TGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: TGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGG-AAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|31558808|gb|CD528020.1|CD528020
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|67010625|gb|CO439374.1|CO439374
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|149112806|gb|EE295616.2|EE295616
EST:     CCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCGGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|32945066|gb|CF049885.1|CF049885
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGAAAATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|37397542|gb|CF636072.1|CF636072
EST:     TGCCCCTTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: TGCCCC-TACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|148996194|gb|EE035466.2|EE035466
EST:     CTGCCCCTCCCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|4837470|gb|AI670560.1|AI670560
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|211311765|gb|FL424550.1|FL424550
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|60672264|gb|DN475030.1|DN475030
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
EST: gi|109637413|gb|EC590958.1|EC590958
EST:     CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG                         AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC
genomic: CTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGAC

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: 129

CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 285

CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 266

CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2366

CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagt ... cacttgccagAAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttccttgaactgtatacaaactgacatcaattcatattctgatatctgacagcatgtttcacttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA