Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctccacacagattacactgaacattgttgctggaagatgtttcgctgagactaccgactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT

Basic information

species Zea mays
transcript GRMZM2G108285_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 5
--tcctccacaca-gattacactgaacattgttgctggaagatgtttcgctgagactaccgactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT
   |    | | | || |   | | | | | |  |  |||| |||      ||   |   | |  |     ||     || |||| |   || | | |  |||||||||||||||||||||||||||| |||||||||||    |||||||| || ||||| || || ||||| ||||||| ||| ||  |||| ||||||||
acacaaatagatacgactgttcgggatact-tcaccagaag-tgtaagaacgaacattatgccgccctgcactgaaacctgtttcttacctc-tcatctgcagTTGACTACCTGCTGTTCATCGTCCGCGACGTGAAGGTAGTCCCGAACCCGGACGAAGTGGCCGATGTGAAATACGTGAGCCGTGAGCAGCTGAAGGAGCT

upper sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 5
tcctccacacagattaca-ctgaacattgttgctggaagatgtttcgctgagactaccgactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT
        | | |  |   || || | | ||| |      | | | |   ||| ||   |   || | |||  || || | | | | ||||||     ||||||| ||| |||| |||||||| || ||||||||||| || || |||||||||||||| |||||  | ||||| |||| ||| || ||||| ||||||||
------gtaaataccatttctcaagactcttggttcccattttcttgaacagaataataaaaccttaagcttctt-ctgtgttggccttcctttt--gcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAGATGAAGTAGCTGAGATCAAGTATGTGAGCCGGGAAGAGCTGAAGGAGCT

upper sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 5
tcctccacacagattacactgaacattgttgctggaagatgtttcgctgagactacc--gactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT
              || ||    | |   || | ||  || | ||  |   ||| |    ||| |  ||  |   |    |   |  |||  || |    ||||||||| || || |||||||| ||||| |||||| | || || |||||||||||||| |||||  | |||||||||| | | || ||||| ||||||||
-------------gtaaacaatccttccatgtttgatcatttctctttttaactcctttaacttcagattttgaatctcttgaggatttttgttgc----agTTGACTATCTACTCTTCATCGTGCGGGATGTGAAGCTTCAACCAAACCCAGATGAAGTGGCTGAGATCAAGTACGTGAGCAGGGAAGAGCTTAAGGAGCT

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|60359625|gb|DN226598.1|DN226598
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33102488|gb|CF062448.1|CF062448
EST:     CCGAATGCTTTACAAGGCGCCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33102495|gb|CF062455.1|CF062455
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33101212|gb|CF061172.1|CF061172
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCGGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33100629|gb|CF060589.1|CF060589
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGGGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|24765500|gb|CA400659.1|CA400659
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|5740029|gb|AI947719.1|AI947719
EST:     CCGAATGCTTTACAAGGCNCCATCTGCCGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|60358782|gb|DN225755.1|DN225755
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|84977083|gb|DW475505.1|DW475505
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33101179|gb|CF061139.1|CF061139
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTTCCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|24770101|gb|CA405230.1|CA405230
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|14203887|gb|BG837564.1|BG837564
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAAGGTGCAGCCGAACCCA
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAA-GGTGCAGCCGAACCCA
EST: gi|29130604|gb|CB381308.1|CB381308
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCT
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCT
EST: gi|18659800|gb|BM500528.1|BM500528
EST:     CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGC                         TTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33101189|gb|CF061149.1|CF061149
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
EST: gi|33100900|gb|CF060860.1|CF060860
EST:     CCGAATGCTTTACAAGGCACCATCTGATGGGAAATGGGGGGAGCATGAGC                         TCGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG
genomic: CCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 444

CTGGGCATCCCAGCAGAAGATGCCCCAGTTGACCAATTCACCCCTCTGGGCCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1739

CTGGGCATCCCAGCAGAAGATGCCCCAGTTGACCAATTCACCCCTCTGGGCCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1583

CTGGGCATCCCAGCAGAAGATGCCCCAGTTGACCAATTCACCCCTCTGGGCCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 846

CTGGGCATCCCAGCAGAAGATGCCCCAGTTGACCAATTCACCCCTCTGGGCCGAATGCTTTACAAGGCACCATCTGACGGGAAATGGGGGGAGCATGAGCgtaagtttct ... ttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgagactaccgactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT
                                          tccttac  putative branch site (score: 846)
                           ttgctctttcgtcttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctccacacagattacactgaacattgttgctggaagatgtttcgctgagactaccgactgctaatgctagttgctctttcgtctttccttaccatcagTTGACTACCTGCTGTTCATCGTCCGGGACGTGAAGGTGCAGCCGAACCCAGATGAAGTCGCTGACGTGAAGTACGTGAACCGCGACGAGCTCAAGGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-cctccac
- - - - - - - - cactgaa
- - - - - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - - - - - atgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gactgct