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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctgaaatctcacaacaagctgttcgcttggctttaatccgaaatggcttctactgattgtacagtgtttataccttttaattgtccctcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGCAGGCCCCTGGTGCTTCAGGTGCAGAGGCTGGCGCCAGCGCTGGTGCTGC

Basic information

species Zea mays
transcript GRMZM2G131577_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131577_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 3'ss of exon 5
---gacctgaaatctcacaacaagctgttcgcttggctttaatccgaaatggcttctactgattgtacagtgtttatac-cttttaattgtccctcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGCAGGCCCCTGGTGCTTCAGGTGCAGAGGCTGGCGCCAGCGCTGGTGCTGC
      ||||||| |   | |||     |  || |||  |||       |    | |      |||  |   ||      | |||  || | |||||| | |||| ||||||||| | || || |||||||||||||| ||||||||||| |||||||| ||||||||||| |||| ||||||||| ||||| ||||| |||||
aatttactgaaatgttgaagcaa----cttactgggccataacttaccctcatctttgaaagctgttgaagcttcgcttacctttgtttattcctcctattcagGTCCTGACAACTTGGATAATCTGCGGAGGCTTGCAGAGCAATTCCAAAAGCAGGCTCCTGGTGCTTCTGGTGAAGAGGCTGGTGCCAGTGCTGGAGCTGC

upper sequence: GRMZM2G131577_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 3'ss of exon 5
gacctgaaatctcacaacaagctgttcgcttggctttaatccgaaatggcttctactgattgtacagtgtttataccttttaattgtccctcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGCAGGCCCCTGGTGCTTCAGGTGCAGAGGCTGGCGCCAGCGCTGGTGCTGC
     |   |   | |  |   | | |  ||   | |  ||     || | | ||    || | |  | | |||   ||| || | |  |        ||| || || ||| | ||||||||| ||| ||| || ||||| |||||||||||||| ||||||||    | ||  |  || |  |||   |  | || || 
-gtacgttcttctagattactttttccattttcttcttttct----tgccctttatccttttttccatttatatttttttaaactttttc--------agGACCAGATAACTTGGACAACCTGAGGAAGCTGGCTGAGCAGTTCCAGAAGCAGGCACCTGGTGCAGGGGCTGGTGCAGCAGCAGCCCAAGACGATGATGA
















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|78085080|gb|DV513473.1|DV513473
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|211115551|gb|FL427475.1|FL427475
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGAAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|18384847|gb|BM418046.1|BM418046
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|18175340|gb|BM350693.1|BM350693
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|60400816|gb|DN233623.1|DN233623
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|37392111|gb|CF633302.1|CF633302
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|18659819|gb|BM500538.1|BM500538
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|91871711|gb|EB401668.1|EB401668
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|29544321|gb|CB604701.1|CB604701
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|37386069|gb|CF630208.1|CF630208
EST:     AGCTGCAAGATCTGCTCCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|67018429|gb|CO447178.1|CO447178
EST:     AGAAGCTGTAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGAAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|76924262|gb|DV169881.1|DV169881
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|86471797|gb|DY238167.1|DY238167
EST:     AGCTGCAAGATCTGTTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|37386066|gb|CF630206.1|CF630206
EST:     AGCTGCAAGATCTGCTCCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|22489532|gb|BU049455.1|BU049455
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|211143800|gb|FK990190.1|FK990190
EST:     AAAGAAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AAAGAAGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|211233416|gb|FL467936.1|FL467936
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|16920324|gb|BM074598.1|BM074598
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|19436302|gb|BM952712.1|BM952712
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|50332820|gb|CO527946.1|CO527946
EST:     AGCTGCAAGATTTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|18384733|gb|BM417932.1|BM417932
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|67020870|gb|CO449619.1|CO449619
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|37388804|gb|CF631614.1|CF631614
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|16745989|gb|BM032419.1|BM032419
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCTATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|18384732|gb|BM417931.1|BM417931
EST:     AGCTGCAAGATCTGCTTCCATCGATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCCTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|78083088|gb|DV511481.1|DV511481
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
EST: gi|86474995|gb|DY241365.1|DY241365
EST:     AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCG                         GCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC
genomic: AGCTGCAAGATCTGCTTCCGTCCATTATCAACCAGCTCGgtacgttttt ... tcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcttctactgattgtacagtgtttataccttttaattgtccctcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGCAGGCCCCTGGTGCTTCAGGTGCAGAGGCTGGCGCCAGCGCTGGTGCTGC
                                      ttgtccctcct  CT-rich tract
                        tttataccttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctgaaatctcacaacaagctgttcgcttggctttaatccgaaatggcttctactgattgtacagtgtttataccttttaattgtccctcctgtgcagGCCCTGACAACCTAGACAACCTGCGGAGGCTTGCGGAGCAATTCCAGAAGCAGGCCCCTGGTGCTTCAGGTGCAGAGGCTGGCGCCAGCGCTGGTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC