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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 12
gtaaagtattaagaccttggtttgcaagatttt--gaatgctagataaatcta--acataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
|||| |||||| |||| |   |  || ||||||   |||||  || ||   ||  | || |||| ||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||
gtaa-gtattaggaccgtcagtcacatgattttcaaaatgccggacaagcatatcatatgaaaaccatatttcagGTGCCTACTGGGTGGAAATTTTTTGGGAACTTGATGGATGCTGGAATGTGCTCAATTTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
---------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaac--ataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
                      | |||||| || |   | ||| |   | ||||  |      || | | ||    ||    |        ||||| || || || ||||| || ||||| ||||| |||||||||||| | || ||| |||||||||||||||| ||||| ||||
gtatattgctcttcaatgtcttttaagtatgaaaatacttgtt-gatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
                                | | |  |  ||     |   ||  |||||      ||||| || || || ||||| || ||||| ||||| ||||||||| || | || ||| |||||||||||||||| ||||| ||||
-------------------------------gtaattattttatttgattgttattcaaaac------cagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
--------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtt---tcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
                     | ||| || || |   | | | || |  ||| ||    ||  ||  | |||  |||  |  ||       ||||| || || || ||||| || ||||| ||||| |||||||||||| | || ||| |||||||||||||||| ||||| ||||
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaatta--tttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------gtaaagtat-taagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
              | ||  | | |    | |   ||  |   | |    |   ||  |  || |  |    ||| ||  | |||||| || || || ||||| |||||||| ||| ||||||||||||| ||||| ||  | ||||| |||||||| ||||| ||||
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
--------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtt-tcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
                     || | | ||  |  | |  | | | | |  |   | |    ||| || |   ||  |        |  ||||| || ||||| |||||||||||||| || || |||||||||||| | || ||||| |||||||||||||| ||||| ||||
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatga-gaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
            |   | || ||||    || |   ||||     |  |   | || |      ||| ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||| || ||||||||||||||||| || || || |
------------gtgataggattgct--cttgttcttgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
     ||  || ||  |   ||       || |   ||||     |  |   | || |      ||| ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||| || ||||||||||||||||| || || || |
-----gtgataggatttctctt------gttct---tgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

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|116816329|gb|EC859054.1|EC859054
EST:     CAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAG                         GTGCCTACTGGGTGGAAACTAAACGGGAATCTGATGGATGCTGGAATGTGC
genomic: CAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAGgtaaagtatt ... catgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGC
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     CAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAG                         GTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGC
genomic: CAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAGgtaaagtatt ... catgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
                              atctaac  putative branch site (score: 2)
                       tagataaatctaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA