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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt...

Basic information

species Zea mays
transcript GRMZM2G142334_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgt--accttctgata---cttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt
|||||||||||| || |||||||||||||| || ||||| |||||||| ||||| ||||||||||| ||||||||||||||||| |||||||| ||||||||||||||| ||  ||||  ||| |   ||| |  | | | | || |  ||    || | |  |  ||| |     | | ||||  ||  | ||    |  ||  
TTCAAGATCATTCTTTACTGAGATTATAGCCTCGATTTCAGACATAAAGTTTTCCAAGGATGGGAGACATATTCTCAGTCGTGATTACATGACACTGAAGgtctgtaccagtttacctgttgacatccctttactttttattgatct-tagtcatcaagaagcattgattatgt--tggatattacttggctacatcatgctt--

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgt-acctgtaccttctgatacttcaaatataaataatttgcagctgacatg--taaaaaagatgagacccttgctattcttttaccaccctgttttttt-
 ||| ||||||||||||| |||||||| || ||||| || ||||||||||||  ||||||||| ||  |||| || |||||||| ||||||||  | ||||| ||  | || |||  |   | | | ||    |   | | | | ||||    ||  ||     ||||      || || |   ||||      ||   |    
GTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTTAGTCGTGATTACATGACCTTAAAGgtttgagagctttactattccaaaatacatgcttctgtcaat-gaagcttttctgagtattttggatggag---ttactctaaatttattgaattgaactccat

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctatt----cttttaccaccctgttttttt----
 || |||||||||||||| |||||||| ||||| || |||||||||||||||  ||||||||| ||  | || || |||||||| ||||||||| | ||||| || |     |  |||| ||  |  |||| ||     | ||       | |  | || |  |  ||| ||||  |||    |  ||| |    | ||||||     
GTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaa-----attttctaat-ttcaaaatctatgctttctgttaa-agctttcacaatattttggactcttggaattaggacccttaac-ttttattttttaaaac

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt-------------
 || |||||||||||||| |||||||| ||||| || || ||||||||||||  ||||||||| ||  | || || |||||||| ||||||||| | ||||| || |     |  |||| ||  |||||| || |||  ||| | | | |   |  || |   || ||       |||| ||||| |  |  || |||||             
GTCCAGATCATTTTTCACAGAGATTATTGCTTCTATCTCAGACATAAAATTTGGGAAGGATGGAAGATACATACTAAGTCGTGATTACATGACTTTAAAGgtttgga-----attttctaat--ttcaaa-atcaattcttt-ctgttaaagggagaatattttgggaatg----tatttttttaactactagtatttttcaattagcaagaa

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G20830.3 (Glycine max), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtct-gtacctgtacc-ttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt-
 || |||||||||||||| |||||||| |||||||| || ||||||||||||  ||||||||| ||  |||| || |||||||| ||||||||  | ||||| |   | || ||   |||  | ||      |      |||       |     |||     ||||      || || |   ||||      ||   |    
GTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTTAGTCGTGATTACATGACCTTAAAGgttttagagctttattattccaaaacccatgcttctgtcaataaagcttttctgagtattttggatggag---ttactctaaatttattgaattgaactccat

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtacc-ttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctatt--cttttaccaccctgttttttt---
|||||||||||||||||| ||||| || || |||||||| || || ||||| || |||||||||||  | || || ||||| || |||||||| || |||||  | |    | |  |||   |  |  | || |   | |||    ||  | |       |   |      ||| ||  |  ||||||||    |     |||   
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTTAGTCGCGATTACATGACGCTCAAGgttggaaatcattcggttccctttgtgtatatttttctgattgtgggccaatagaggtctattctttagttctttctgatatcttttaccctttttgacgtttcag

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt-----
|||||||||||||||||| ||||| || || |||||||| ||||| |||||||| |||||||| ||   ||| |||||||| || |||||||| || ||||| ||        | || |  || |    || | |    ||  ||  |||| || ||        |  |  |  ||  | | |       || |  | |      
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTCAGTCGAGATTACATGACCCTTAAGgtttgggttatcccatttttctattc---atttcagc--ttcacatttgacttgaaacttttgcaattctatcactgctatatatgggtgctttagtctagagtg

upper sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 9
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 9
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaat---aatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt
 ||||| || |||||||| || || || ||||||||||| ||||| || ||| | |  | ||   || ||||||||||||| |||||||||| |||||||||  ||     ||  |   | || |   ||| | | |    ||||  | |    | || ||    ||||          |     | |  |    ||  ||  
ATCAAGGTCTTTTTTCACAGAAATCATTGCTTCAATTTCTGACATTAAGTTTGCAAGAGGTGATCGGTATATTCTCAGTCGGGACTACATGAGTCTGAAGgttagttatattaaatctagctattctgaatgtgagttgtgatttatatcgctgaagtgaagcttatgaagtaacaag-acctcgtaaagaatgagtaatt--

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|32806442|gb|CD958676.1|CD958676
EST:     TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAG                         CTTTGGGATGTTA
genomic: TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTA
EST: gi|67016408|gb|CO445157.1|CO445157
EST:     TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAG                         CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT
genomic: TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT
EST: gi|71417754|gb|DR804198.1|DR804198
EST:     AGTCGGGACTACATGATTCTGAAG                         CTTTGGGATGTAAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT
genomic: AGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT
EST: gi|6020391|gb|AW065319.1|AW065319
EST:     TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAG                         CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT
genomic: TTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCAT

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), 46 (downstream exon)
Score: 150

TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 87

TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 146

TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacct ... attattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTCAGTCGTGACTACATGACTCTGAAGgtctgtacctgtaccttctgatacttcaaatataaataatttgcagctgacatgtaaaaaagatgagacccttgctattcttttaccaccctgttttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaga