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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattccgcaaatttgttgaagtttttaattccaatcacacttttggtacatatttaagaaactcttatctttttgttttttccaaacgaatttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

Basic information

species Zea mays
transcript GRMZM2G011923_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 3
tgattccgcaaatttgttg-aagtttttaattccaatcacacttttggtacatatttaagaaactcttatctttttgttttttccaaacgaatttgct-----tagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG
 |   |   |  ||  |   ||  || || ||  |||||    | |    || ||   |||||||   |  || |||||  |   ||  |  ||||||      ||||| | |||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
-gggactttattttgctcataaacttctatttgtaatcaacaatgtacccca-at---agaaactaacaggttattgttgctat-aactgtttttgctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G25870.2 (Glycine max), 3'ss of exon 3
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggta--catatttaagaaactcttatctttttgttttttccaaacgaatttgct-tagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG----------------
    | || |  |   |  ||    | || |  ||  |   | ||| ||  || | ||||       | ||  |||  ||  ||  |||    | || |  |||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||                
---attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAGGTAGTAGAATATAGGA

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggtaca-tatttaaga-----aactcttatctttttgttttttccaaacgaatttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG
    | |    ||   ||    || ||| ||  || |||  ||    || | |   ||| |     ||   |||  |  || |||  |      ||| ||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||
----ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgc--agGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG

upper sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggta--catatttaagaaactcttatctttttgttttttccaaacgaatttgct-tagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG
    | || |  |   |  ||    | || |  ||  |   | ||| ||  || | ||||       | ||  |||  ||  ||  |||    | || |  |||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||
---attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG

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|22490259|gb|BU050182.1|BU050182
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|18655190|gb|BM499995.1|BM499995
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|29544431|gb|CB604811.1|CB604811
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|149107938|gb|EE292294.2|EE292294
EST:     CAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|31351065|gb|CD435422.1|CD435422
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|31352279|gb|CD436636.1|CD436636
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|31352997|gb|CD437354.1|CD437354
EST:     TAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCCCTGCATGGGAGGATAAG
genomic: TAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|29544031|gb|CB604411.1|CB604411
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|87152915|gb|DY397704.1|DY397704
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|31351326|gb|CD435683.1|CD435683
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|148982112|gb|EE028161.2|EE028161
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|149102032|gb|EE287514.2|EE287514
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGGATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGAT
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGAT
EST: gi|37399688|gb|CF637177.1|CF637177
EST:     TCTTTTTCTTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: TC-TTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|149107040|gb|EE188934.2|EE188934
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGGTGG-TCTAATATTGAT
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGG-TGGGTCTAATATTGAT
EST: gi|60350260|gb|DN217233.1|DN217233
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|78087740|gb|DV516133.1|DV516133
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|40303492|gb|CK347879.1|CK347879
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|45567374|gb|CK985540.1|CK985540
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|31352510|gb|CD436867.1|CD436867
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|149082225|gb|EE171408.2|EE171408
EST:     AGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: AGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|60401294|gb|DN234101.1|DN234101
EST:     ACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: ACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|211413346|gb|FL280968.1|FL280968
EST:     CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTCGGTGGGTCTAATATCGATCCCACTGCATGGGAGGATAAG
genomic: CTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
EST: gi|60358053|gb|DN225026.1|DN225026
EST:     CACCAGCTTCATGGGGTATTTGAG                         GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG
genomic: CACCAGCTTCATGGGGTATTTGAGgtgtgtgatt ... atttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtacatatttaagaaactcttatctttttgttttttccaaacgaatttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG
                                              tttgctt  CT-rich tract
                    ttatctttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggtacatatttaagaaactcttatctttttgttttttccaaacgaatttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT