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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcttctattgtcattaatactactgtttggtactgtccattctgtttcatgtagtctatataacgcctttatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 4
gtaatatcttctattgtcattaatactactgtttggtactgtccattctgtttcatgtagtctatataacgcctttatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG
|||||||||| | || |      ||||||  |||| | || |   || || || |||   | ||||  || | ||    ||  ||||| |||||||||||||||||||||| ||||| ||||||||||| ||||| ||||||
gtaatatcttgttttat------tactacaatttgctccttttt-ttttgcttgatgcgatttata--accctttctcattgcagGCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG
















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|60399773|gb|DN232583.1|DN232583
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|211186705|gb|FL252850.1|FL252850
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|5895762|gb|AW037008.1|AW037008
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|14242681|gb|BG840373.2|BG840373
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGANTAAA-TGGG
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGA-TAAAATGGG
EST: gi|211436012|gb|FL361903.1|FL361903
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGAATGATAAATTGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|211186703|gb|FL252848.1|FL252848
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|13178078|gb|BG349336.1|BG349336
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|211186707|gb|FL252852.1|FL252852
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTTCACATT                         GCACGACCAACCATATATC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATC
EST: gi|76010926|gb|DT938096.1|DT938096
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|60355084|gb|DN222057.1|DN222057
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|32918930|gb|CF023742.1|CF023742
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATG
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATG
EST: gi|71774337|gb|DR972215.1|DR972215
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|78113266|gb|DV531659.1|DV531659
EST:     TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     TTCTGATGGCGGCTATTCGTAATGTCCACATT                         GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC
genomic: TTCTGATGGCGGCTATTCGTAATGTCCACATTgtaatatctt ... tatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggtactgtccattctgtttcatgtagtctatataacgcctttatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG
                                 atataac  putative branch site (score: 3)
                                       cgccttt  CT-rich tract
                                           tttatgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcttctattgtcattaatactactgtttggtactgtccattctgtttcatgtagtctatataacgcctttatgttatagGCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA