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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA

Basic information

species Zea mays
transcript GRMZM2G094978_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 4
agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaa-gcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA
|  |     || ||  |   |  || |   ||||| |    |   ||  |  || | ||  | ||  |  |    | |  | |    ||  |||| | |||||||| |||||||| || |  ||| |||| |||||| | || || || |||||||||||||||||||||||||||||||  ||||||||||| |||
atgtactatttttcacactttttaaatagtagtacatgttgatagtagct-gtgaacttgtatgccagatagctcacatatttatgcttgactgaatgcagGTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA
















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|91056651|gb|EB167069.1|EB167069
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|211136606|gb|FL156037.1|FL156037
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCGATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|149095606|gb|EE165515.2|EE165515
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT                         GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT
genomic: TAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCTgtaagtaatt ... ctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA
                                           tcctgat  putative branch site (score: 3)
                                 ctgttctttttcct  CT-rich tract
                        aaactataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatttacattctcttaacatccaactgccagtacttaagaaacttattttatgcaattaaagcagggcaaactataactgttctttttcctgattacagGTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - -cattctc
- - - - - - - - - - - caactgc
- - - - - - - - - - - - - - - - - - taagaaac
- - - - - - - - - - - - - - - - - - - - - - - - -ttatgca