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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttcttgaaacctatggtttttttcatggctcagtgattcttttagtttcttagatacttgattgagtaaagatcgtcgcagactcagcatgcta...

Basic information

species Zea mays
transcript GRMZM2G060800_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g08300.1 (Oryza sativa), 5'ss of exon 4
CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttcttgaaacctatggtttttttcatggctcagtgattcttttagtttcttagatacttgattgagta-------aagatcgtcgcagactcagcat-gcta---------------------------------------
|| || || ||||| | ||| || || ||||| ||||||||| ||||||||||||||||||||||||| ||||| |  |||||||||||||||||||||||| || |||||       || |||||       ||| | ||||| ||||  ||| ||   |       || |||       ||  |  ||    | || |  | |||                                        
CCTGAATACGTTGATAGCTCTTGCATAAAAGTGGTGGAGGGAGGCGTTCCAGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttcttatcttgcatagttttccagtatgct-aatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcag

upper sequence: GRMZM2G060800_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S272_3V6.1 (Physcomitrella patens), 5'ss of exon 5
CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttcttgaaacctatggtttttttcatggctcagtgattcttttagtttcttagatacttgattgagtaaagatcgtcgcagactcagcatgcta
||    ||  | |||||||||   |||   || ||||| ||  ||||  | ||||| |||    | |||||||||| |||||||||||| ||||||||||||    ||  |   |  ||       | |||  || |  |  |  ||  |  |||| |   |     ||||  |    | |  |  || || |    |  
CCTCTCTACATGGACAACTCCGTCATTCGTGTGGTGGAAGGTGGCGTGGCTGAAACCACCTTGTTGTTGGAACAGAAATGGGATAAGATTTTCTACACAGgtgcgtttagtccgaagtagatcgaatatcaatgcacgat--tctttgcaaattctgaatgaagccgttgacgag---ttgcggttgaatcggttgacag
















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|78123147|gb|DV541531.1|DV541531
EST:     AAAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GAAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
EST: gi|58029607|gb|CX725034.1|CX725034
EST:     AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
EST: gi|6564146|gb|AW231768.1|AW231768
EST:     AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
EST: gi|78121155|gb|DV539539.1|DV539539
EST:     AAAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GTAATGGAACTGTAAGACGTATAGTGATGGCAGCACCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
EST: gi|78111538|gb|DV529935.1|DV529935
EST:     AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
EST: gi|32841121|gb|CD980802.1|CD980802
EST:     AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAG                         GTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA
genomic: AGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGA

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: 73

CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 525

CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttct ... gaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGAGTATGTTGACAACTCCTGTATTAAAGTTGTGGAGGGAAGCGTTCCAGAAACAACCGCACTCTTGGAACAGAGATGGGATAAGATCTTCTACACAGgtcaagttcttgaaacctatggtttttttcatggctcagtgattcttttagtttcttagatacttgattgagtaaagatcgtcgcagactcagcatgcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG