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

gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

Basic information

species Zea mays
transcript GRMZM2G149272_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 3
-------------gtgcgctcttatct-----cccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
              |     || ||||      |  |  ||||| |    ||   |  | |||| |||||   || | ||| ||  |        ||||   | ||| | ||| || || |||||||| ||||||||||||||||||||| |||| || ||||| || ||||| |||||||| || || |||| |||||||||||||||||| 
gtctgtatagtctatatatactgatctagcagtctcttttgctgttgc-cgccatgtctcgcaagttgctcggaacactgacattgg--------aacgatct-gatgtgtagTGTGGTTGAGAGTGTTGGTGAAGGTGTGACCGAGTTCGAAGTGGGAGACCATGTGCTCACCGTCTTCATCGGAGAGTGCATGAGCTGCAAGCACTGCGTT
















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|211521058|gb|FL044641.1|FL044641
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211521056|gb|FL044639.1|FL044639
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211353144|gb|FL044621.1|FL044621
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCNGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACC
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTC-GGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACC
EST: gi|211355542|gb|FL044630.1|FL044630
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211521054|gb|FL044637.1|FL044637
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211353142|gb|FL044619.1|FL044619
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACC
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTG-TCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACC
EST: gi|211355543|gb|FL044631.1|FL044631
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211521055|gb|FL044638.1|FL044638
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211353139|gb|FL044616.1|FL044616
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCCG                         AGTAGTAGAGAGTGTCGGGTGAAGGTGTGACCGA-TTCCAAGTCGGTGACC
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGG-TGAAGGTGTGACCGAGTTCCAAGTCGGTGACC
EST: gi|211355544|gb|FL044632.1|FL044632
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211355540|gb|FL044628.1|FL044628
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAAGTAAAGAGTGTCGGGTGAAGGTGTGACCGAGTTCCCAAGTCGGGTG
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTA-GTAGAGAGTGTCGG-TGAAGGTGTGACCGAGTTCC-AAGTCGG-TG
EST: gi|211353143|gb|FL044620.1|FL044620
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTATAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211355546|gb|FL044634.1|FL044634
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAAGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTC-AAGTCGGTGAC-A
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|50322631|gb|CO517757.1|CO517757
EST:     GCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211521057|gb|FL044640.1|FL044640
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAAAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGAACA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211355545|gb|FL044633.1|FL044633
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211355535|gb|FL044623.1|FL044623
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
                                       cgccttc  CT-rich tract
           ttctaataatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC