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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggctacatatgctgttattataccgtgcatgacgtgagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 6
-gttggctacatatgctgttattataccgtgcatgacgt-gagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG
 |    || | |  |      |  ||  |  | |||  | || |     || |||   |  |    | | ||||  ||    ||   ||| |  |||  ||||||||||| |||||  | ||||||   || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||
tgagtactgcttcagtaaaagtcttattgaacttgagctagatatgtgataaatcatctttagttatttgtgttgtttcc--ctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
















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|5846756|gb|AI999839.1|AI999839
EST:     CCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     CCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     TGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: TGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     ACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: ACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG
                                        tccattt  CT-rich tract
     atctattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctacatatgctgttattataccgtgcatgacgtgagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG