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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac

Basic information

species Zea mays
transcript GRMZM2G146786_T01
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
||| |||||||| || ||||| ||||| |||||||||||||| ||||| |||||||| |||||||| | |||||||||||| ||||||||||||||||||||||||| |  |  |  |||     | || ||| | |  || |   || |||| |          || | ||  |  ||||||        | ||     ||   |||                                                                                    
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtaca-gtttcatgaaaaaa-------aaaaagggactattagctcaat--atagctcaaaccagtcttatg----------------------------------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaaca-actttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
||| |||||| | ||||| || ||||||||||||||||| || || |||||||| ||||| || ||||  ||||| || |||||||||||||| |||||||||||||||  |  ||||    | || |  |  | | ||||      |    | |    | ||| | || |   | |  |     | ||  ||     | ||                                                                                           
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgattt---ttatgtcctactactacaattaccttgct------------------------------------------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G33570.2 (Glycine max), 5'ss of exon 4
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaaca-actttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
||| |||||| | ||||| || || |||||||||||||| || || |||||||||||||| || ||||  ||||| || |||||||||||||| |||||||||||||||  |  ||||    | || |  |  | | |||| |    || ||  |  |||    || |||  | |   |  |   | ||    |||    | | |                                                                                        
CAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgttttcttcttcatcttg-ggttgatttgatactgatttttatgtcctact----actacaagtatc----------------------------------------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatc--aacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
 ||||| ||||| ||||| |||||||| || |||||||| || ||||||||||| || |||||  | |  |||||||| ||||| |||||||| ||||| ||||||||| ||||        | | | |   |||      ||     ||    |||   |    |  || |  ||  || | ||||  ||   |  | || |                                                                                           
TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcac-------------------------------------------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 5'ss of exon 4
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
             || || || || ||||| ||||| ||||| || |||||||| |||||| | || |  || |||||||| || |||||||| |||||||||||||||  |   |        ||||   ||| |   | |  |  | | | |  ||     | | |  |||| || |||||  |    ||  || | |||    | ||    | |||  || |    |||                                                            
------------ACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGCATTTAAGATATCCTTTCGTgtgc--------ctttagatttgcaactgtgtacattagggt--ggctgtgtcattggggttgagatagctcgt----aatgttctggca----tgca----aattttattgcaaaaaaaag----------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 5'ss of exon 5
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggt-tcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
 |||||||||||||||||| |||| || |||||||||||||| || ||||| |||||  | |  || |  || || ||| | || ||||| |||||||| ||||||| |    |||    | |    ||  |||| |    |  |  |||  |     | | |  | | |||| | ||  |||     |      ||  |||    |                                                                                      
TAGCGATGATTTGCTTTACTTGAAGGAACAAATGGAAGCTGAGGAGGATGCCGAGCGTTTGCGCCGGCGAACGGAAAAGAGAGCGTTTGCAGCTTTTAAAatatcctctg--gatctcttata-tgctggatttcatcgggtgtatctaagaac----tataacaagtttggtgtaagagagcccacttaatggattggcgctgagt--------------------------------------------------------------------------------------

upper sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
-------CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctt-tattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
        || ||||||||||||||| | |||||||||||||||||||| || ||||| |||||  | |  || |  |||||||| ||||| || || |||||||| |||||||| |   | | ||  |  |  ||  | |  | ||  |||| |     |   ||  |   ||| |  ||      ||   |  | ||                                                                                                     
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtcaga--agtgatggtagag----------------------------------------------------------------------------------------------------

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|211273251|gb|FL384319.1|FL384319
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211532797|gb|FL373547.1|FL373547
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTG
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTG
EST: gi|211082871|gb|FL417813.1|FL417813
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACC
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACC
EST: gi|74239761|gb|DT647675.1|DT647675
EST:     GCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: GCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211536312|gb|FL400261.1|FL400261
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211413441|gb|FL400135.1|FL400135
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211334889|gb|FL419773.1|FL419773
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211385044|gb|FL404090.1|FL404090
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTC
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTC
EST: gi|211421419|gb|FL412843.1|FL412843
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|32943201|gb|CF048020.1|CF048020
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCTGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211024425|gb|FL373964.1|FL373964
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211527056|gb|FL387984.1|FL387984
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211500127|gb|FL425199.1|FL425199
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTC
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTC
EST: gi|211346219|gb|FL403635.1|FL403635
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|93016518|gb|EB642038.1|EB642038
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211271661|gb|FL410597.1|FL410597
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|211039375|gb|FL382073.1|FL382073
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|89758028|gb|DY687371.1|DY687371
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCTGATTCTACACCTGGTGGCCCTGGGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
EST: gi|33771049|gb|CF273343.1|CF273343
EST:     CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAG                         AAAGCAGCAATTTTAGCCGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT
genomic: CAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatccttta ... ctgacattacAAAGCAGCAATTTTAGCTGATTCTACACCTGCTGTCCCTGTGGCTCTTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT