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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt...

Basic information

species Zea mays
transcript GRMZM2G047431_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgc-ctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt
|||| ||| ||||||||| ||||||||||||||||||||||| || || ||||||||||||||||||||||||||||||||||| || || |||||||||||    | |    | |   | | |||  ||  || |   ||||||||| |||  || ||   | || |      |||||  |      ||  |||   |  
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctc-tctctctctcccgcccggatcgatctagctagggcatcgcgtca

upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagat-cgcgccctggtggttatccatttt
             ||||||| || || ||| ||||||||| ||||||| || |||||||||||||| |||||||| || |||||||| ||  ||||||||||||    |  |         | |  ||   | |  | |  |   |||     |||   |  | |||  ||  | |   ||     |              
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaatt--ttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag--------------

upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 5'ss of exon 2
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacg-acgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt
                 | | |||||| |||||||||||||||||||| || || |||||||||||| |||| ||||| || || ||||||      ||||| ||  ||      | |  |||       |   ||   |   || | | ||   ||  |||| ||    ||   | |  |     |              
----------------AACGAGGAGTATGACGTGATCGTGCTGGGCACGGGTCTGAAGGAGTGCATCATCAGTGGCCTGCTGTCGGTGGACAAGAAGAAGgtgcgggacctagacatgcgcgcgaatgctgcaaccgggcctgcttttcttcgcgcgctggccgctcaccatcgcaacctgttgcag--------------

upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 1
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgta-cgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttc-taataagatcgcgccctggtggt-tatccatttt-
| || |   ||| |||||||  || || |||||||| ||||| ||||| || |||||||| ||||| ||||| || || ||||| || || |||||||||||  |||  | || |  |||   ||   | ||  |     | | | |  ||  |   | |    ||||    | || | |     | | | |  |    |  | 
CGGCACCTTCGCTATGGATGAAGATTATGACGTGATTGTGCTCGGCACTGGCCTCAAGGAATGCATTCTCAGTGGACTGCTCTCCGTTGATCGCCTCAAGgtggcgtctccctccctcga--tctgggttga--catgtgtgtgtgtagcttggagattgatagcttcgcgttcaggttgaatgtttgagatgcaagtgtgctg

upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S167_1V6.1 (Physcomitrella patens), 5'ss of exon 1
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcg--gcca--cttctaataagatcgcgccctggtggttatccatttt
  | ||  || |||||||||  |||||||| ||||| ||||||||||||||||| ||||||||||||||||| || || ||||| ||||| || ||||||||  ||       |    |   |    | ||||       |||   |  |  | ||| |  |||     |||      | || |   | |||||   | |    
TGGAGCCGGCACCATGGATGAAGAGTACGATGTGATTGTGCTGGGCACCGGGCTGAAGGAGTGCATCCTCAGTGGGCTACTCTCCGTGGATCGTCTCAAGgtgggtgggatcgc----agatcgtggttgatctgtgtgactcgggcggtgtggcgtagctgccggctctctgggtgtagcgtggatttgtggtcggcgaggga

upper sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt
      | |||||||||||| |||||||||||| || |||||||| || || ||||||||||||||||||||||| || || || ||||| || ||||||||  |||   ||    ||  |     |   ||| |   | |                                                           
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------------------

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|33771077|gb|CF272738.1|CF272738
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
EST: gi|110506044|gb|EE017844.1|EE017844
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCCCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCCT
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGC-T
EST: gi|33771056|gb|CF273350.1|CF273350
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
EST: gi|211323781|gb|FL062365.1|FL062365
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
EST: gi|148960309|gb|EE153565.2|EE153565
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
EST: gi|211323782|gb|FL062366.1|FL062366
EST:     GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
EST: gi|37621893|gb|CF674946.1|CF674946
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACCGCCTCAAG                         GTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTC

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: 48 (upstream exon), 47 (downstream exon)
Score: 64

CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTCAATCTCAATCAG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 82

CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTCAATCTCAATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTCAATCTCAATCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 123

CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacg ... atgtcatcagGTGTTGCACATGGACAGGAATGACTACTACGGCGGAGACTCCACATCGCTCAATCTCAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcgccc