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

gtaagaccacctgtcaatattttttatttcaagtgcaatgattttcaagtcgttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC

Basic information

species Zea mays
transcript GRMZM2G466281_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 6
gtaagaccacctgtcaatattttttattt-caagtgcaatgattttcaagtcgttgtgagct-----cattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC
||||| | |     |||  ||| |   || || || | |  ||    ||    |||||| ||      |||| ||||||||| ||||||||  |||||||||||||||||||||| ||||||||||| ||||||||||||| |||||||||| | |||||||||||||||| ||||||||||||||
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC

upper sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
-----gtaagaccacctgtcaatattttttatttcaagt--gcaatgattttcaagtcg-ttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC
      ||  | ||    |  |   ||| | ||| || |  | | |  | ||  ||||| || |||     ||||      | |  |||||||| || |||| ||||||||||| || ||||||||||  | ||| |||||||| ||| | ||||||||| | ||||||||    || || |||||||
gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaa--ggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC

upper sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
--gtaagaccacctgtcaatattttttatt-tcaagtgcaatgattttcaagtcgttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC
   |         |||| ||  || ||||| |  |||      |  || |   | ||   | || || || | | |     |||||||| || |||||||||| ||||| || ||||||||||   || | |||||||| ||| | ||||||||||| |||||||| |  ||||| |||||||
gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtcttt----cagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC

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|101388019|gb|EB816024.1|EB816024
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTT-GGAAGCACGGCGATGTGTGGAAAGG-TAACCTT
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTA-CCTT
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGACGCACGGCGATGTGTGGAAAGGCTATCTTC
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTC
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     CGGATGTGATGCGCTTGCGTGTGCT                         TTTGAATCCTTGGCTTTTGGAAGCA
genomic: CGGATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCA

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: 23 (upstream exon), 48 (downstream exon)
Score: 190

GATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC


Block sizes: 23 (upstream exon), 49 (downstream exon)
Score: 171

GATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 157

GATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC


Block sizes: 23 (upstream exon), 49 (downstream exon)
Score: 221

GATGTGATGCGCTTGCGTGTGCTgtaagaccac ... tatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaagtgcaatgattttcaagtcgttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC
                                  ctcattttttttat  CT-rich tract
                                   tcattttttttatata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccacctgtcaatattttttatttcaagtgcaatgattttcaagtcgttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG