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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaactgtgagaaatatcggttccatgtttctgaaatctgtatatagttattgacatttagaatgacgtgtatattatactagttttcaacatt...

Basic information

species Zea mays
transcript GRMZM2G146677_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 5'ss of exon 8
GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaactgtgagaa-atatcggttccatgtttctgaaatctgt---atatagttattgacatttagaatgacgtgtatattatactagttttcaacatt
|||||||||||||| |||||||||||||||||||||||   ||||||||| |||   ||||||||||| |||||||||||||| ||||| ||||||||||| | ||   ||| ||  || |  |||  ||  | |||| || ||   ||  |  |  |  || ||  ||  |  ||         | |     ||  || 
GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTCGAAGGCCTAGGTTCACCATTGTCATGGGATCACATCACCAATCAGgtaaaga-aatcatgaaaatgtaccatttc--tgaatatgaattcagtgacatgcaaattataccagttcaaagtagttgccagcatctccaaggcccacaat-
















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|31349057|gb|CD433414.1|CD433414
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|6056460|gb|AW090850.1|AW090850
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|31362346|gb|CD446703.1|CD446703
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|32908144|gb|CF012957.1|CF012957
EST:     GTCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|32833423|gb|CD973101.1|CD973101
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|31353746|gb|CD438103.1|CD438103
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|211235538|gb|FL127822.1|FL127822
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|5714296|gb|AI944281.1|AI944281
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|5847048|gb|AW000127.1|AW000127
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|31352769|gb|CD437126.1|CD437126
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|84977385|gb|DW475807.1|DW475807
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGACATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|50324321|gb|CO519447.1|CO519447
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|5846903|gb|AI999986.1|AI999986
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|18172785|gb|BM348173.1|BM348173
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|211237763|gb|FL127823.1|FL127823
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|211237764|gb|FL127824.1|FL127824
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|5296287|gb|AI783057.1|AI783057
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
EST: gi|32834200|gb|CD973878.1|CD973878
EST:     ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG                         ATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA
genomic: ATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTA

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: 46 (upstream exon), 43 (downstream exon)
Score: 13

GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 52

GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 25

GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG


Block sizes: 47 (upstream exon), 38 (downstream exon)
Score: 30

GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaa ... ctctgtacagATTGGAATGTTCTGCTACAGTGGGATGACACCTGAACAAGTTGACCGTTTAACAAATGAATACCACATTTACATGACCCGCAATGGGAGGATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAGgtaaatacaactgtgagaaatatcggttccatgtttctgaaatctgtatatagttattgacatttagaatgacgtgtatattatactagttttcaacatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaata