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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc...

Basic information

species Zea mays
transcript GRMZM2G064695_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc-
|||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||| || ||||| || ||||||||   | || |   ||| |  |   | |  ||   ||   |     |   | |||   | ||| |    |  |         ||  |||| |     ||  
GACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTGGAATAGTGAATGCAGCAAAACAGgtttgtcttcaaattttgtatgtagttttcatttaatgactaaagcagcttattgtggttccctct-tgcttcaaattaataaattacaatatacctattg

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcata------ccccccacccccctccccccccaacaacaacaacagaatc
|||| | ||||| | ||||||||||||| | || ||||||||||| || || ||||| |||||||| |||||||||||||| || |||||||| ||| ||||   |||   |||| |     | |     | || |||  |   ||| ||    |  ||       |    || ||   |  |  ||      |||| | | |   
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagttt---gcctattcccccctcccacaaaaaataaataaatgaaaaaacagaaatcttatgtctttacaaccagttttcttcctttgtccaaccatata---

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgt---------acatttttagccttt---cttagctttatgtataacataggttcctg---acaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||| | ||||| | ||||||||||||| | || |||||||||||||| || ||||| |||||||| |||||||||||||| || |||||||| ||| ||||         |||| |  |  ||||    ||      |||||  |  |   ||  ||   || ||||||   ||                   |  ||                
GACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaagaacatgtaaattctttatatttgatcccatgtaagatttcaatttttgtttacgatgttgatgtaattgttgatattacaatttctgaaa---------------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagc--ctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
||| || || |||| |||||| |||||  | |||||||| |||||||| || ||||||||||||||||| || |||||||| || || ||||| ||| ||||   |    | |  | || ||| | | || | |  ||||  ||| |||     |    |||   || |      |        ||   | |  ||||    
GACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTGGAATCGTGAACGCTGCAAAAGAGgtgagtgagaaacaaccttgttaccataatattt--catatattcatgat----tgaaaataaatccgagt---gtttgtgtggaatggcgaggacag----

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagct----ttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||| | |||||||  || || |||||| |||||||||||||||| || || |||||||||||  | |||||||||||||||||||||||||| ||| |||||   | |    |    || | |    || |||  |  |     |  ||   ||  ||||  |       |    |   | | | ||  |   |  |      
GACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctgcatcaagattggttcagattctgttgattacctacttttgctcatagtggc-cattaaat-cttgtcatgctctctaattatgtcttctagt--

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S9_103V6.1 (Physcomitrella patens), 5'ss of exon 10
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattt-ttagcctttcttagctttatgtataacataggttc---ctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc
|||||| ||    |||||||| || ||||| ||||||||||||||||| || ||||| |||||||| || ||   |||||||||   |||||| ||||||||| | || |     | |   ||    |||| |  |  || ||    |   ||||  | | |     |  |         |    ||  | ||    ||     
GACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgtctaagtgtggcagaagaatgttttgctgagttttgttccttcaatactcgtaacattctgatatggaagtctatacataagcatgttcat----

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: 587

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 945

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1054

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 857

GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacattttt ... ccgttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTGGAATTGTTAATGCTGCCAAACAGgtacatttttagcctttcttagctttatgtataacataggttcctgacaatgttggcataccccccacccccctccccccccaacaacaacaacagaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaacaa