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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcatatactcttccgaatattccatgagtgcctgtagcaatgtaatgaagcattgtcttattctataggaatgacatgct...

Basic information

species Zea mays
transcript GRMZM2G145709_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 5'ss of exon 3
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcata-tactcttccgaatattccatgagtgcctgtagcaatgta-atgaagcattgtcttattctataggaatgacatgct-
|||||||||||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| ||| |||||||| ||| ||||| ||| ||| | |  || |||| | |  | |||||| | || || ||||||||| || ||| |  ||  || |  ||     |||  | || 
ACTAACCTGGTCAATCTAATTGGCTATTGTGCTGATGGTGACCAGCGCCTTCTTGTCTATGAGTTTATGCCATTGGGATCACTGGAAGACCATTTGCATGgtttgtctatcttctccttgcctttctagtcttgcaag-agtccatgggcgcttgaagcaatgtacataaagta--gtagtactgcattattgtgaagtacta

upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G10360.1 (Glycine max), 5'ss of exon 3
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctcttt-----gtcatatactcttccgaatattccatgagtgcctgtagcaatgtaatgaagcattg--tcttattctataggaatgacatgct
 | || || || ||  |||||||||| |||||||||||||| || || || ||||||||||| |||||||||||||| ||  | || |||||| | || |||| |  |   | || |||     |  || |   ||||   |  |    ||  | | | |   ||    || ||  |||   | | ||  |||   |||        
CCAAATCTTGTGAACTTAATTGGCTATTGTGCTGATGGTGATCAGCGGCTGCTTGTTTATGAATTTATGCCATTGGGATCTTTGGAGGATCATTTACACGgtcagattgctttcttttttaactgatatctttgcttcttcaactattgtgctttcatattataaaactataaaatattaaatttcatgttatttcaatc-------

upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G28730.1 (Glycine max), 5'ss of exon 3
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcatatactcttccgaatattccatga--gtgcctgta-gcaatgtaatgaagcattgtcttattctataggaatgacatgct
 | || || || ||  ||||||| || |||||||||||||| || || || ||||||||||| || ||||||||||| ||  | || |||||| | ||||||| |  |   | || ||| | |   |  | |  |  | ||| || |  |||| |  |    ||  |   |   | | | | |||  ||    ||   ||   
CCAAATCTTGTGAACTTAATTGGTTATTGTGCTGATGGTGATCAGCGGCTGCTTGTTTATGAATTCATGCCATTGGGATCTTTGGAGGATCATTTACATGgtcagattgcattcttttt-taactgatacctttgcttcttcaattatagtgctttcatattataaagctataaaatatttaatttcatgttgattcaatc--

upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcatatactcttccgaatattccatgagtgcctgtagcaatgtaatgaagcattgtcttattctataggaatgacatgct-----
 | || || || ||| | ||||| || ||||||||||| ||||| || |||||||| ||||||| ||||||| | || ||| | || |||||||| || ||| ||  ||       ||   ||    ||   |     ||| ||| | |  |  ||  |   |||  || | |||  || || | |   | |  ||||       
CCCAATCTTGTGAATTTGATTGGTTATTGTGCTGATGGGGACCAGCGTCTTCTTGTGTATGAGTATATGCCACTAGGATCATTGGAGGATCATCTACACGgtatgcttagtgatatttccccact--cttaacatggaattgcattattttccataaga---taagaaacctttgcatttttatttgaaactaccatggaccgaa

upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 5'ss of exon 3
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgt----catatactcttccgaatattccatgagtgcctgtagcaatgtaatgaagcattgtcttattctataggaatgacatgct
 | ||||| || ||  | ||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||| ||| | || |||||| | ||||||  |  |  || |  |||||     |  || |   ||  | ||  ||  ||    | | || || |  || |   | |    |   |   |  ||   ||   
CCAAACCTTGTTAACTTGATTGGTTATTGTGCTGATGGGGACCAACGTCTGCTTGTCTATGAGTTTATGCCATTGGGATCATTGGAGGATCATTTACATGgttagattgcctgccttttgtgcactagttattaacccataaataacaaaagacagttttgctattttttgca-tgtagatcaaccatgctgtcatttgat---

upper sequence: GRMZM2G145709_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S478_1V6.1 (Physcomitrella patens), 5'ss of exon 3
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcatatactcttccgaatattccatgagtgcctgtagcaatg--taatgaagcattgtcttattctataggaatgacatgct
|| || || || ||||||||||| ||||| ||||||||  | ||||| || || || || ||||||||||| |||||||   | ||||| ||||||||||||  ||| | |     |   || ||   |  |   |    |      |  | || ||   |   | | |  |   ||        | | |   |  ||    
ACGAATCTTGTAAATCTAATTGGTTACTGCGCTGATGGCCAGCAACGGCTGCTAGTGTACGAGTTTATGCCGTTGGGGTGCTTGGAAGACCATCTGCATGgtaagtgaagcggag-tggatcgtaggatggtgataggggttggcagggacgtgaagtggtcgttgacgtggtggtggggaccattgtggctttcgcag---

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|149106246|gb|EE291941.2|EE291941
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
EST: gi|76291614|gb|DV031182.1|DV031182
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
EST: gi|89758504|gb|DY687662.1|DY687662
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
EST: gi|148942135|gb|EC887138.2|EC887138
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAAATAAAGAGCCTCTTGATTG
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTG
EST: gi|148941217|gb|EC886109.2|EC886109
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAG
EST: gi|148938285|gb|EC882589.2|EC882589
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGGCCACC
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTG-CCACC
EST: gi|33467045|gb|CF244094.1|CF244094
EST:     TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATG                         ATCTGCCACCAGATAAAGAGCCTCTTGATTGGAA
genomic: TCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAA

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: 308

ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAACACCTTCATGACAAGGCGAGTCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 343

ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAACACCTTCATGACAAGGCGAGTCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 234

ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAACACCTTCATGACAAGGCGAGTCC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 221

ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtat ... atttgtatagATCTGCCACCAGATAAAGAGCCTCTTGATTGGAACACACGGATGAAGATAGCTGCAGGTGCAGCTAAGGGCTTAGAACACCTTCATGACAAGGCGAGTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAACCTGGTCAATCTAATTGGCTACTGTGCTGATGGTGACCAACGCCTTCTTGTTTATGAGTTTATGCCATTGGGGTCACTAGAAGATCATCTGCATGgtctgtgtatctcctctttgtcatatactcttccgaatattccatgagtgcctgtagcaatgtaatgaagcattgtcttattctataggaatgacatgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA