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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatattgttattattggactgcttatctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA

Basic information

species Zea mays
transcript GRMZM2G137528_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 2
------aaatattgttattattggactgcttatctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA
        | ||||| ||| | |  ||| |   |      ||   ||||| | | |||| || ||| ||  ||  ||| ||| |||||   |||  ||||  ||||||||| || |||||||||||||| || ||||| ||||| ||||||||||| |||||||||||||||||||||||||| |||||||| |||||||||||||
gatctgtcacattgtcatt-tggttctgttagccc---tttttgtaatggaaatcctaaatttctgtttacca--gtgctattaacttctcaatataattattcagGTACATCCAGAAGGCAAATATGTGGTGGATATTGATAAAAGCATTGATATTACAAAGATCACACCTTCAACAAGAGTTGCTCTTCGAAATGATAGCTATA

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
aaatattgttattattggactgcttatctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA
            ||| | |    || | | | |||  |     | | |||||    | | |||||||    |   |  |||  |       |||   ||||| || || || || || |||||||||||||| || || || || || || || || ||||| || ||||| ||||| ||||||||||||||||||||| 
-----------gtat-gaatcttttttattatcatgttt----gtatttctacgaacatagttgtcagtaaggcttacactccc-------attttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 2
-------aaatattgttattattggactgcttatctgagcattctca-atgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA
        |  ||| || || |  | |||  | |   |   || | |  |  ||  | | | |||  | |  |     |||||  |  || ||        |  | |||| || || ||||| || |||||||||||||| ||||||| ||| || ||||| |||||||||||||||||  |||| |||||||| ||||| |||||| 
atttctctaccatt-ttcttttacggctgaatttaacaatgttgtgatgtatgaaatgtgagttca-gatgatttggctgataatattttcctt------ctttttagGTTCATCCAGAAGGGAAGTATGTTGTTGATATTGATAAGAACATAGACATCACTAAGATCACACCTTCAACCCGAGTTGCTCTTCGCAATGACAGCTATG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 2
aaatattgttattattggactgctta---tctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA
   | |   | |   |  | |   ||    | ||       || ||   | | |   |  ||  ||   |  ||  |||  || ||||  |     || ||||||||| || ||||| || |||||||| ||||| || |||| ||| |||||||||||||||||||| ||||| ||||| ||| | || |||||||||||| 
-gttgtctgtgtgggtacattttgtagaacccgatagcaaacagtgtatggttttcttgtctcatttctatggt--tattcaccttcttttccttgtgttcagGTACATCCAGAAGGGAAGTATGTTGTAGATATTGACAAGAACATAGATATCACAAAGATCACACCATCAACTAGAGTTGCTTTACGGAATGATAGCTATG

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|32828073|gb|CD967751.1|CD967751
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|20208241|gb|BQ134330.1|BQ134330
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCGAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTCGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|19350715|gb|BM895247.1|BM895247
EST:     AGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: AGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|211028259|gb|FL437884.1|FL437884
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|19350732|gb|BM895264.1|BM895264
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|32805431|gb|CD957665.1|CD957665
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|32866277|gb|CF005959.1|CF005959
EST:     GTTGGTGAGGTGGTGAAGGTCATGGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: GTTGGTGAGGTGGTGAAGGTCAT-GGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|9742895|gb|BE519043.1|BE519043
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCGAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
EST: gi|32827753|gb|CD967431.1|CD967431
EST:     ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG                         GTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC
genomic: ATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAGgtaatttttt ... aattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA
                                   tttctaatgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatattgttattattggactgcttatctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA

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