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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacag

Basic information

species Zea mays
transcript GRMZM2G176546_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 17
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaa---atttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacag
|||||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||| |||  |||||    |||||||||||||||||| | |||||||||   || |   |  ||   |    |     |||    | ||  || || ||     | || |||  || ||||||| ||||  | |||
AAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAACgtaacgtatcttgctatgtatttctgtctcctatttaagttcaaatatattaaat---gagtt-tcagaaattacatttgaaaacatgcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 16
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagc-tttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacag
|||||||||| || ||||| ||| |||| ||||||||||||||||| |||||||| |||||||  ||||||   ||||||||||| || ||| | ||||||||| || ||||   |  ||      ||   |||  | | |   || ||  |     | || |||  || || |||| |||| || |||
AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctatatatttctatcttctactatttaaattcataaatatttgat---gagtt-tcagcaattaaatttgaaaacctgcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 17
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaact-gca-acttatcaataaatacattttaa--aaacta--cag
||||||| ||||||||||||||||| ||  |||| ||||| ||||||||||| || || ||  |  | || |  |||||  | || |||||||  || |||||| |  || |||    ||        ||||  || |||||||  || | || |||   |||  | ||  |  |||| ||  ||| |   |||
AAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGGTTATCACAAAGATGAAGCCCAGACgtaattacctttcctgttctgt------gcttctta-tgaatgaaatttaccttgcatgtttaaaagtacttgaatttcaatcaaattgagcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 17
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgca-acttatcaataaatacattttaa--aaacta--cag
||||||| ||||||||||||||||| ||  |||| ||||| ||||||||||| || || || ||  | || | ||| ||  | || |||||||  || |||||| |  || |||    ||           || || |||||||  ||    ||||   |||  | ||| |  |||| ||  ||| |   |||
AAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGGCTATCACAAAGATGAAGCCCAGACgtaattacctttcctgttct-------gtgcttctaatgaatgaaattaccttgcatgtttaaaagtaattgaatttcaatcaaattgagcag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 17
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagctt---tgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaacta-cag
||||||| || |||||||| ||||| || ||||||||||| ||||| |||||| | || || ||  | || |  |||||| |||| |||||||| || |||||     ||  ||    ||      |   ||   |||  || ||  | |  || |   |   |||  | | ||  |  | |||   | |||
AAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatc--tgattatgtgatcaaattgaacag

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S12_178V6.1 (Physcomitrella patens), 5'ss of exon 20
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttc---tatccgtcac------ttaaacatagctt--tgtactgaatgatcttcaac--tgcaacttatcaataaatacattttaaaaactacag-----------------------------------------------------------
| ||| | || |||  | ||||  | ||||||||||| ||||| |||||||| |||||||| ||| ||||| | || ||||| || || |||||| ||||||| |||||   |   | ||||      ||  | |||  ||    |||  ||  |||||| |   |   | || | ||    |     || |   | ||                                                             
AGATGGAGTACACAGATAATGACAAGCCTTATCCTCGAGGAGAGATTTGTGTGAGAGGACCCATATTATTCAAAGGCTACTACAAAGACGAAGTTGAAACgtagatttcatgttctcttcacgcgtctttggatatacgttgtcatacctaagtatcttcgatgatttgaattgtgaacctctgacagttgactccaacgcatattaatatcctactttttattacttaagctgatgttcttgtgaatttcttattgtag

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|6194573|gb|AW146677.1|AW146677
EST:     GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAAC                         AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
genomic: GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
EST: gi|67023162|gb|CO451911.1|CO451911
EST:     GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAAC                         AAAAGAAGTCGTTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
genomic: GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
EST: gi|6194494|gb|AW146598.1|AW146598
EST:     TTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAAC                         AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
genomic: TTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
EST: gi|211216802|gb|FL024787.1|FL024787
EST:     GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAAC                         AAAAGAAGTCMTTGATGAAGATGGTTGGTTGC
genomic: GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGC
EST: gi|91873018|gb|EB402975.1|EB402975
EST:     GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCCAAC                         CAAAGAAGTCATTGAATGAAGATGGTTG
genomic: GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGA-TGAAGATGGTTG
EST: gi|50335868|gb|CO530994.1|CO530994
EST:     GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAAC                         AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT
genomic: GTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCT

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), 48 (downstream exon)
Score: 78

AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 309

AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 149

AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttct ... aaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG