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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaatattatttgtatttgacctttttctgattattgaattttcttagaacaacatattatgtatttttatatacaatgagtatatcatggactat...

Basic information

species Zea mays
transcript GRMZM5G844173_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 5'ss of exon 7
GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaatattatttgtatttgacctttttctgattattgaattttcttagaacaacatattatgtattttt---atatacaatgagtatatcatgg-actat---
|||||||| |||||||||||||||||||||||||| | || |||||||| ||||||||||| ||||||||| |||| ||| |||||||||||||| |||||||||| ||| ||  ||    | || | ||  || |   || |    || | ||    | ||  |   || ||   | ||||||     || | ||||   |||   
GAAATGAACCTGACCGGAAGCCATTGAGGCCACTATCTCCTTGGATCACAGACATATTGCTTGCTGCACCTCTGGGTATTAGAAGTGACTATTTTAGATGgtgagtcataataaatga---taacatattattgttctgtgga----ctgaaaatctgaaatcctcctttcttgagaaatacaacctcaattttatggtgatattga

upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G36600.1 (Glycine max), 5'ss of exon 6
-GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata-ttatttgtatttgacctttttctgattattgaattttcttagaacaacatattatgtatttttatatacaatgagtatatcatggactat
 || |  |   |||   ||| ||  | |||||  |  |||| ||||| ||||| || ||| | ||| ||||  | || ||||||||||||||||| |||||||||||| |  |||   ||| | ||   |||      |||| | ||  |    |  |    || ||||||   | |||    | | | |       | |  
TGACAC-AGCATGAGAAGAAACCTATAAGGCCGTTGTCCCCCTGGATTACTGATATTTTGTTGGCTTCACCAGTAGGTATTCGAAGTGACTATTTCCGATGgtgagtatttcttaaaagtaatagataatttagct-ctatttatttggccagaagtagttaatcatgtatgcatgtatgttttaactttgcttgcaagtcc

upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 6
GAAATGAATCTG-ACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaatattatttgtatttgacctttttctgattattgaattttcttagaacaacatattatgtatttttatatacaatgagtatatcatggactat--
   ||| | | | |   ||| ||  | || ||  |  |||| ||||| ||||| ||||| | |||||||||||| |||||| |||||||||||||||| ||||||||| | ||  || |   |      |     ||  ||    ||  || |    | |||     ||||  || || | |||    | | | |  ||    
-TGATGCAGCAGGAGAAGAAACCTATAAGACCCTTGTCCCCTTGGATTACTGATATATTACGAGCTGCACCTTTAGGCATTAGAAGTGACTATTTTCGGTGgtgagtatttttcattatgcctacaaagtcatgtatggttttgcttctttcggttcagatagatgatattagta-atgctatgtacgtttta-gttctgcct

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|32842002|gb|CD981683.1|CD981683
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842384|gb|CD982065.1|CD982065
EST:     GACATATTGCTAGCTGTACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|148956314|gb|EC902116.2|EC902116
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842680|gb|CD982361.1|CD982361
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842398|gb|CD982079.1|CD982079
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842301|gb|CD981982.1|CD981982
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842595|gb|CD982276.1|CD982276
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842361|gb|CD982042.1|CD982042
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842489|gb|CD982170.1|CD982170
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32922209|gb|CF027021.1|CF027021
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32923012|gb|CF027824.1|CF027824
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32842370|gb|CD982051.1|CD982051
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32841992|gb|CD981673.1|CD981673
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
EST: gi|32841997|gb|CD981678.1|CD981678
EST:     GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATG                         GTGTGGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC
genomic: GACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCC

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: 47 (upstream exon), 47 (downstream exon)
Score: 54

GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 36

GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 36

GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 72

GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaata ... catatatcagGTGTAGCGGTGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGAATCTGACCGGAAGCCATTGAGGCCACTAACCCCGTGGATCACTGACATATTGCTAGCTGCACCTTTGGGCATTCGAAGTGACTATTTTCGATGgtgagtaatattatttgtatttgacctttttctgattattgaattttcttagaacaacatattatgtatttttatatacaatgagtatatcatggactat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaca