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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatccgatgtttctctttgttgttcgtccttccatgtgcatcattgccaactttcagattgtcaacaactgatattgtctcatttgttttgttaactcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAATTATCCACTGCTCAATTTCATGCTGACTACTGCTATATATGTTGCG

Basic information

species Zea mays
transcript GRMZM2G020721_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 13
gtaaccatccgatgtttctctttgttgttcgtccttccatgtgcatcattgccaactttcagattgtcaacaactgatattgtctcatttgttttgttaactcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAATTATCCACTGCTCAATTTCATGCTGACTACTGCTATATATGTTGCG
||||||| | | |||  ||||    | ||    |     |  |   || |   |  |      ||||       ||  | || || |    || | || |||||||||||||||  ||||||||||| ||||| |||||||||||| |||||||||||||||| ||| |||| ||||||||||| || ||||||||||||||||| 
gtaaccagctgctgt--ctctacaatattacctccgtggttcgtgccactagaagttcctc--ttgttc----ttgtcaatgactgaaa-attgtctttactcctgcagATCAAAAGTGCCCAATGGGCAACCTAAATGGCTATTGACAATAATCCCAAATTACCCAATGCTGAATTTCATGCTCACAACTGCTATATATGTTGCA
















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|94472577|gb|EB701535.1|EB701535
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5847621|gb|AW000700.1|AW000700
EST:     GGAAAGATTACTCTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATT
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATT
EST: gi|5325022|gb|AI783213.1|AI783213
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5895688|gb|AW036934.1|AW036934
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5901242|gb|AW042342.1|AW042342
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5847179|gb|AW000258.1|AW000258
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|76933472|gb|DV173475.1|DV173475
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|6227096|gb|AW155800.1|AW155800
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCCAAAATGGCTATTGTCAATAATCCCAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACC-AAAATGGCTATTGTCAATAATCCCAA
EST: gi|5895689|gb|AW036935.1|AW036935
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|86473236|gb|DY239606.1|DY239606
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|71762483|gb|DR960420.1|DR960420
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5343255|gb|AI795560.1|AI795560
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5846835|gb|AI999918.1|AI999918
EST:     AAGATTACACTAGNAAACATANCATATCTCAGTTCCATTATCTGGCTCAG                         N
genomic: AAGATTACACTAG-AAACATA-CATATCTCAGTTCCAT-ATCTGGCTCAGgtaaccatcc ... actcctgcag-
EST: gi|5846835|gb|AI999918.1|AI999918
EST:     AAGATTACACTAGNAAACATANCATATCTCAGTTCCATTATCTGGCTCAG                         N
genomic: AAGATTACACTAG-AAACATA-CATATCTCAGTTCCAT-ATCTGGCTCAGgtaaccatcc ... actcctgcag-
EST: gi|32936459|gb|CF041278.1|CF041278
EST:     GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: GGAAAGATTACACTAGAAACATACATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
EST: gi|5455799|gb|AI833489.1|AI833489
EST:     ATATCTCAGTTCCATATCTGGCTCAG                         ATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA
genomic: ATATCTCAGTTCCATATCTGGCTCAGgtaaccatcc ... actcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttcagattgtcaacaactgatattgtctcatttgttttgttaactcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAATTATCCACTGCTCAATTTCATGCTGACTACTGCTATATATGTTGCG
                                        tgttaac  putative branch site (score: 2)
                                              ctcctgc  CT-rich tract
                                atttgttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccatccgatgtttctctttgttgttcgtccttccatgtgcatcattgccaactttcagattgtcaacaactgatattgtctcatttgttttgttaactcctgcagATCAAGTGTGCCCAATGGCCAACCAAAATGGCTATTGTCAATAATCCCAAATTATCCACTGCTCAATTTCATGCTGACTACTGCTATATATGTTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG