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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaatctttacacttacatacaattagtttttttttttgtagaaacaatctttgatctttatttttactgcag

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaatctttacacttacatacaattagtttttttttttgtagaaac-aatctttgatctttatttttactgcag
|||||||||||| || |||||||||||||| ||||||||||||||||||||||| || |||||||| ||||| |||||||| |||||||||||||| |||||| || |      |   |||  | | |||  || | | || ||||||||   | |||| ||| | ||  | |||||||
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagtta-----caagtttattt-ctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcag

upper sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttgg-----taaatctttacacttacatac--aattagtttttttttttgtagaaacaatctttgatctttatttttactgcag----------------
|||||| ||||| |  ||| | ||  | |||||||||||||| ||||| |||||||| || ||||||||| ||||| |||| || |||||||| |||||||| |        ||| |  ||| |  | | |  |  |  |    || ||| | ||||||    |  || | |   ||    | ||                
TGAAGATGCTGTGCCTTGCATAGCGCTATCGAAGAATGATTCTTATGTGATGTCCGCCTCGGGAGGAAAAGTCTCTTTGTTCAATATGATGACATTCAAGgtagagcttacgaatttagacattggctttctcagctgatgaacttgtttat-gaaacagcgatgcatttctggcttctaggaagttcgctttgtttcttt

upper sequence: GRMZM2G550865_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaatctttacacttacatacaattagtttttttttttgtagaaacaatctttgatctttatttttactgcag
 ||||||||||| |  ||| |||| ||||| |||||||| || || || ||||||||||| ||||| ||| | ||||| ||||| |||||||||||||||||  | | || ||| |   |  |      ||     ||    |||  |                              
GGAAGAAGCTGTGCCTTGCATTGCCTTGTCAAAGAATGACTCTTACGTGATGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccag-----------------------------

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|18963627|gb|BM660541.1|BM660541
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         C
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcag-
EST: gi|18963627|gb|BM660541.1|BM660541
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         C
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcag-
EST: gi|22546038|gb|BU098359.1|BU098359
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|19058178|gb|BM736845.1|BM736845
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|87152018|gb|DY396807.1|DY396807
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|32858467|gb|CD998148.1|CD998148
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|67032677|gb|CO461426.1|CO461426
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|87157645|gb|DY402434.1|DY402434
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|26558945|gb|CA831180.1|CA831180
EST:     TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT

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: 265

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 151

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCCGCTTCTGGAGGAAAAATCTCTCTGTTTAACATGATGACTTTCAAGgttggtaaatctttacacttacatacaattagtttttttttttgtagaaacaatctttgatctttatttttactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA