Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccctacttacagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagtacatag

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T05 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 5'ss of exon 10
CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccctactt---acagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagtacatag
|||||||||||| ||  | || || ||| || |||||||||| ||||| || ||| |||||||||||||||||||||| |||||||| ||||||||||||||  ||||||   |   ||| ||    ||   | | ||    || | |  | || ||||     |   |   || | |||||   | |||                                                                                       
CCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCTTCACCTTGACACCAGAGCAGgtggctccctcagtgacacacttggcccatcctcttaagctatactcatgcttt-tctaaatctcaccgtcgtcttcttcaactatgcag---------------------------------------------------------------------------------------
















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|78179647|gb|DV550020.1|DV550020
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|32840610|gb|CD980291.1|CD980291
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|76289739|gb|DV029307.1|DV029307
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|116822883|gb|EC866344.1|EC866344
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCAT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCAT
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|32839672|gb|CD979353.1|CD979353
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGCCAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|5915565|gb|AW053206.1|AW053206
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGTACATAG                   
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACC--AG-AG--C--AGgtaactccct ... cagt
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagT-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 6

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... cagtacatagTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG




<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccctacttacagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagtacatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG