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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaatagtgtagcatgttttgattggttgcacgtttgattgtagcatggttgctgtggtgtcatcatataccttaccaagtgggttttcatctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTCAATCTGCCTGGTGGGATACCCGAATCATGGCCGAAGTTACTGCAGGCCC

Basic information

species Zea mays
transcript GRMZM2G150014_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150014_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 3
aaaaatagtgtagcatgttt---tgattggttgcacgtttgattgtagcatggttgctgtggtgtcatcatataccttaccaagtgggttttcatctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTCAATCTGCCTGGTGGGATACCCGAATCATGGCCGAAGTTACTGCAGGCCC
     |  | |   ||||     |||   | || |     ||  ||   |   ||  | |  | |       | || | |    |  | | |||| |||||||  ||| ||||||||||| ||||||||||||||||| |||||  ||||||||||||| || || || || || ||||||||||||||||||||||| ||  
--ttgtcttattttatgtgcaaatgaaaagctgaataagggaaagtt-tacatttagtttactttggcatcgtgccgtcctctctaagctgtcatttttgcagTGTGAGCCAGTGGAGGACTTCTACAGAGCACGTGGTAAACTATTGGAGTTCAATCTACCAGGAGGAATTCCAGAATCATGGCCGAAGTTACTGCAAGCAT
















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|32938115|gb|CF042934.1|CF042934
EST:     ACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|211475867|gb|FL467332.1|FL467332
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|71771574|gb|DR969511.1|DR969511
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|76928642|gb|DV171706.1|DV171706
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTTTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|60345933|gb|DN212906.1|DN212906
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|211305869|gb|FL436424.1|FL436424
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|14243925|gb|BG841559.2|BG841559
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|101386808|gb|EB815421.1|EB815421
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTTTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|21331461|gb|BQ486842.1|BQ486842
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|76284881|gb|DV024449.1|DV024449
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|101388895|gb|EB816429.1|EB816429
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|9255052|gb|BE345520.1|BE345520
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|9730993|gb|BE509745.1|BE509745
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|91048681|gb|EB159099.1|EB159099
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|71762227|gb|DR960164.1|DR960164
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTTTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|71760794|gb|DR958731.1|DR958731
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|211305868|gb|FL436423.1|FL436423
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|93284435|gb|EB676699.1|EB676699
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC
EST: gi|71771844|gb|DR969781.1|DR969781
EST:     ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTG                         ACTGAACCAGTGGAGGAGTTTTACAGAGCACGTGGGAAACTGCTGGAGTTC
genomic: ACGATACTGAAGAAGTGGTAAAAGAGCGGCTGCGTGTGTACCATGATTTGgtagggtgtg ... atctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggttgctgtggtgtcatcatataccttaccaagtgggttttcatctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTCAATCTGCCTGGTGGGATACCCGAATCATGGCCGAAGTTACTGCAGGCCC
                         accttac  putative branch site (score: 3)
                                        ttttcatcttt  putative PPT
                  atcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatagtgtagcatgttttgattggttgcacgtttgattgtagcatggttgctgtggtgtcatcatataccttaccaagtgggttttcatctttgcagACTGAACCAGTGGAGGAGTTCTACAGAGCACGTGGGAAACTGCTGGAGTTCAATCTGCCTGGTGGGATACCCGAATCATGGCCGAAGTTACTGCAGGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG