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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC

Basic information

species Zea mays
transcript GRMZM2G143883_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143883_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g33540.1 (Oryza sativa), 3'ss of exon 1
aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC
|| || ||   |   |    |   | |        |   |  ||||  |||   | |           |    ||||||  |   |       ||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||| ||||| ||    ||||| ||   | ||  | |  || || || |  
aagaccgattaatatctgaatgaatgatcaaagaacaaatgtatctgcaaatcaaacgatcatttctgtaacttgcaaatttcctttgtccatcatgcagGTGAACGAGAACTCGGAGAATCCATACTGGAAAGCAATAGGATACAGAGTGGAAGAGCCCCGACGTGATCGAGCAGAGTCGATGCCGTCGCCGTCGCCAT
















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|76012507|gb|DT939677.1|DT939677
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|149084377|gb|EE173826.2|EE173826
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|78083349|gb|DV511742.1|DV511742
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|71438157|gb|DR819207.1|DR819207
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|50327417|gb|CO522543.1|CO522543
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|76926142|gb|DV170732.1|DV170732
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC
                                          tcttgac  putative branch site (score: 3)
                                    tttctctctt  CT-rich tract
                               aaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca