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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G112865_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 1
gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgc---cgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
   |  | |||   | ||  ||  | |       |    | || || || |  ||     || |   ||| ||||  |||||   |||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||
--gtaccatttggcctcgatccttctctctcgagcgcgagatccgcatctctctgtgtgtgtcggagtca-tggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG

upper sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------gtctcgcttttta--acccgcaccgacgcc-----tgtatcctgttgctctgcgtc-gccttgccgttgatctcactggatttgtctccccgg-cagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
                                           | |||| |  |   |||| | | || | |       |  ||    ||| | ||||   ||  |  ||   |   ||  ||   | |||| || |||||| ||||||||||||||||||||||| ||||| |||||||||||||| || |||
gtctggcttctccgcctctccaaccccatctccccggtctccatttcgcctcgtcgcacccacgctgaagtcatggccctgacccacggctgtccgtctatctctctctttgcccttctctatccctttccctgggcagGACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAG

upper sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 1
---gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
      ||    ||| ||      ||     ||| |  | ||| | ||  | ||   |  | |||  ||    | |   | |   |   || || ||||| |||||| |||||||||||||||||||||| || || || ||||||
gttagttcatactttcacttcattcgttttttgttttgttttgttttgt-ttgcagagatgctgaa-tcgtgcgttcccttttatc--tagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG

upper sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 1
gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggc--agGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
   |   ||  ||          |  | | | |  | ||| |     | |  |||| |   | || | | |  |  || |        || || ||||| |||||| |||||||||||||||||||||| || || |||||||||
--gttagttcatactttcacttcattcgtatttttttttgtttcat-ttggtttgcagagaagctgaatcgtgtgttcccatttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG

upper sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 1
gtctcgctt---tttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctcc----------ccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
|| ||  ||   ||  |      || |  | ||  || |      | |    | ||    || |   |      ||||   |||          ||  ||| || |||||||||||| ||||||||||||||||||| || |||||||||||||||
gtttcaattcaattataagttttccaaatcttgggtcttaccag-ccgtacggactgaatgtagtgtttttaaaattttcttccttattttatgccttcagAACAATGGTGTCGCAGTTGGTGAAGCACGAGCGCATTGAAACCACCGTTGCCAAG

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|211055311|gb|FK981922.1|FK981922
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058276|gb|FK981928.1|FK981928
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055303|gb|FK981914.1|FK981914
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055307|gb|FK981918.1|FK981918
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058285|gb|FK981937.1|FK981937
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|22521341|gb|BU080152.1|BU080152
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058284|gb|FK981936.1|FK981936
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|32909297|gb|CF014109.1|CF014109
EST:     GCCGCGATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGC
genomic: GCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     CTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: CTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055308|gb|FK981919.1|FK981919
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|161593639|gb|EY965001.1|EY965001
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGC
EST: gi|32909298|gb|CF014110.1|CF014110
EST:     AAATT-C-CAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTCGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055312|gb|FK981923.1|FK981923
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058281|gb|FK981933.1|FK981933
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055306|gb|FK981917.1|FK981917
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055310|gb|FK981921.1|FK981921
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|78022550|gb|DV490937.1|DV490937
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055309|gb|FK981920.1|FK981920
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|4730329|gb|AI649495.1|AI649495
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058275|gb|FK981927.1|FK981927
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058282|gb|FK981934.1|FK981934
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211061247|gb|FK981940.1|FK981940
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     CAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: CAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058274|gb|FK981926.1|FK981926
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|113702176|gb|EE679680.1|EE679680
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|149097536|gb|EE183416.2|EE183416
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|148963909|gb|EE015021.2|EE015021
EST:     AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211058278|gb|FK981930.1|FK981930
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
EST: gi|211055304|gb|FK981915.1|FK981915
EST:     AAATTCCGCAAGCTTGGCCGCAATTACTCCCAACGCCTCTGCATGCTCAG                         GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC
genomic: AAATTCCGCAAGCTTGGCCGCGATTACTCCCAACGCATCTGCATGCTCAGgtctcgcttt ... tccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
                            atctcac  putative branch site (score: 3)
                                       tttgtctcccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC