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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggtccgtgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC

Basic information

species Zea mays
transcript GRMZM2G063851_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 2
gtgagtggtccgtgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC
           ||| ||  |||| | |   || |||    |   |||   | |  |  | ||    ||||||    ||| | ||||| |||   |     ||||  |  || |||||||| ||||||||||||||||| || |||||||| |||||||||||||||||  | || ||||| 
-----------gtg-agtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcat---ttgtgg----tgtggcgctgaaattccgtt----tgctcgtgttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT

upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 2
gtgagtggtccgtgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC
                      | |     ||        ||  ||  | | | |||      || |||      |    | ||||| |  || | |   ||||  | |||||| ||||| ||||||||||||||||| || |||||| | |||||||||||||||||||| || ||||| 
----------------------gtgagccatccaacatcttgcatgcctattttctggcgatgcgtttgcatttatg--tgcgctgaaaaattgttcgt-tgct--ttgtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGCGCATCTGATCTT

upper sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 1
gtgagtggtccgtgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC
       |   |   ||  |||| | |   || |||    |   |||   | |  |  | ||    ||||||    ||| | ||||| |||   |     ||||  |  || |||||||| ||||||||||||||||| || |||||||| |||||||||||||||||  | || ||||| 
-------gcatggtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcat---ttgtgg----tgtggcgctgaaattccgtt----tgctcgtgttgctgccagGCACAGGAGGCCACCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT

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|211505526|gb|FL228165.1|FL228165
EST:     GGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTSS-ATTCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAG
genomic: GGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGAT-CACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAG
EST: gi|211507876|gb|FL228171.1|FL228171
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507874|gb|FL228169.1|FL228169
EST:     GGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACT--SANTCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAG
genomic: GGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGA-TCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAG
EST: gi|211059244|gb|FL131321.1|FL131321
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|148932412|gb|EC876097.2|EC876097
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507879|gb|FL228174.1|FL228174
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|93284646|gb|EB676910.1|EB676910
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211510249|gb|FL228196.1|FL228196
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|148974563|gb|EE025351.2|EE025351
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211510246|gb|FL228193.1|FL228193
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507880|gb|FL228175.1|FL228175
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507878|gb|FL228173.1|FL228173
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAAGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211510237|gb|FL228184.1|FL228184
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507873|gb|FL228168.1|FL228168
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507884|gb|FL228179.1|FL228179
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211507875|gb|FL228170.1|FL228170
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACT--SATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
EST: gi|211505527|gb|FL228166.1|FL228166
EST:     TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATG                         GCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtc ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC
                  tgctgat  putative branch site (score: 3)
                     tgatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggtccgtgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccagGCGCAGGAGGCCACCACGCTGGGGGGTGTGAGGTGGCTGCAGATGCAGAGCGCGTCCGATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG