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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactgccttattttattccttcgagtatcatcctaaccatagcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG

Basic information

species Zea mays
transcript GRMZM2G147500_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 6
-----gttagactgccttattttattccttcgagtatcatcctaaccata--gcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
      ||    |||| || | |  |  ||  || ||||  ||   |||   || || ||| |||||| | | |    |  ||  ||   |      | | |||  |      |||  |   ||  | |  ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || ||||||
gtagaattgccatgccatagtcttatttttttag-atcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 6
gttagactgccttattttattccttcgagtatcatcctaaccatagcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
                |||    || ||      | || |   | || |  || ||| |  ||  |  |  |      ||   | |  | |    | |||           |||  |  | |  |||||||||   || || ||||| ||||| ||||||||||| || || ||||||||||||||||||
---------------gttagaagtttgatctctttgcttattgtggcgt-cttgtttgg--atgaccctacttcaaaatggataagcctctgactcttgtgaatttgactattgaatggtgttaaagCAAGTAAAGACTCAACAAATGCATGAGATGAAGAAGAAGGAAAAGGAATACATAAAGTTGCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 6
gttagactgccttattttattccttcgagtatcatc-ctaaccatagcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
                |||    || ||   || |  || |   | || | ||  ||   | |    | |   |  |||  || | |  | |    | |||           |||  |  | |  |||||||||   || || ||||| ||||| ||||||||||| || |||||||||||||||||||||
---------------gttagaagtttgatcttctttgcttattgtggcgtcttgtttggatgaccctacttcaaaatgg--ataaagcctctgactcttgtgaatttgactcttgaatggtgttaaagCAAGTAAAGACTCAACAAATGCATGAGATGAAGAAGAAGGAAAAAGAATACATAAAGTTGCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
gttagactgccttattttattccttcgagtatcatcctaaccatagcat-gtttattttgttattgcattgatatttggtgatg-aggtatgttgaacctgtcctgaccttctttggttcttctgc--aagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
                                  |    ||  |    |   |||| | |||| ||| ||| ||| ||   ||| |   ||  | ||    | |  | | | |||| || |  |||  ||||||||  | || || ||||||||||| |||||||| |||||||| ||||||||||| ||||||
---------------------------------gttaggactcttttgttaattatctagttagtgc-ttgttatgtgaaaatgcatagattctaaaagcattc-aatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 6
--------------gttagactgccttattttattccttcgagtatcatcctaaccatagcatgtttattttgttat--tgcattgatatttggtgatga-ggtatgttgaacctgtcctgaccttcttt---ggttc--ttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
               |   |||| |||  |||    ||  ||   || |   |  |||      ||| | ||| |||  ||||||    |     | |    |  | ||  |     ||| | ||  |||   |||||  ||||   |||||||    || ||||| || || ||  | |||||||||||||| |||||||| |||||||||
gtgggtagacaatcttcttactgtcttgatttggagctaagacactcttgaaacacatgcttgttttgtcttgatatcttgcatttccttagtacgctagcagcctattatatacaacctaatctattttacgggttcgattctttcagCAAGTGAAGACTCAGCAGATGCACGAGTTAAAGAAGAAAGAGAAGGAATACATCAAGTTGCAG

upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
lower sequence: PP1S91_39V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------gttagact--gccttattttattccttcgagtatcatc-ctaaccatagcatgtttattttg--ttattgcattgatatttgg--tgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
                      |||| |  |    |||  ||| |    | ||   ||  |     | | | |||| |  |   ||| |     |   ||  |  || | |  | |  | |||||||  ||    | | || || |  ||  |||||||     | ||||| || |||||| ||||||||||||||||||| || || |||||||||
gtgagaagatgttttcgacctctagattttggaagattggatttcagaaaataaggtcattgtttcttggaagtttttcgtaatttacttttcaggacttcaggttggttaaatttactaaacctgttttg--tgtgtgtgtttttcttgtcagCAAGTTAAAGCTCAGCAGATGCATGAACTGAAGAAGAAAGAGAAAGAGTATATCAAGTTGCAG

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|31611780|gb|CD568402.1|CD568402
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATAC
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATAC
EST: gi|22715261|gb|BU197668.1|BU197668
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGA
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGA
EST: gi|211122872|gb|FL004261.1|FL004261
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACC
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACC
EST: gi|211124441|gb|FL004296.1|FL004296
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTANAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGA
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGA
EST: gi|26559425|gb|CA831660.1|CA831660
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGA
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGA
EST: gi|148964224|gb|EE015404.2|EE015404
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATAC
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATAC
EST: gi|26558350|gb|CA830585.1|CA830585
EST:     AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG                         CAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATA
genomic: AGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAGgttagactgc ... cttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
                           tcctgac  putative branch site (score: 2)
                                 ccttctttggttcttc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactgccttattttattccttcgagtatcatcctaaccatagcatgtttattttgttattgcattgatatttggtgatgaggtatgttgaacctgtcctgaccttctttggttcttctgcaagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA