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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccaatgaaacccaaatctgaaccagctagcttcatgagaacaaaagctaaaaccattaagctagtcgattacctgctagattgatttttaactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 3
gccaatgaaacc---caaatctgaaccagctagcttcatgagaacaaaagctaaaaccattaagctagtcgattacctgctagattgatttttaactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT
 |||||   ||     ||   ||||    ||| ||||   | |     |  ||||    |   |   ||   ||||||    | || | ||  || ||||||||||||| ||||||||  ||||||| | ||| ||||||||||| |||||||| |||||||||||||||
tccaatcccactatggaatgttgaatttactaacttcggaatatgttgaagtaaattagtatgg--ggtaagttacctagatgttttaattacaa-tttacagGTTAATAGATGAAGCCCTAGGAAAAGGAGTGAAAGTTGCAGTATGCAGTACTTCAAATGAGAAAGCT
















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:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|211136608|gb|FL156039.1|FL156039
EST:     TGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCCGTCCAG-TGTTCAAAA                         GTTAATCGATGAAGCTTTAGGAAA
genomic: TGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCC-GTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAA
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|211136606|gb|FL156037.1|FL156037
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|149095606|gb|EE165515.2|EE165515
EST:     AAAAGTTGCTTCCTTTCCGTTCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: AAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|86467369|gb|DY233739.1|DY233739
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAG                         GTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC
genomic: ATGGCCCTAATTGAGAAAAAGTTGCTTCCTCTCCGTCCAGGTGTTCAAAGgtcaatattt ... aactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaaaaccattaagctagtcgattacctgctagattgatttttaactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT
                                         ttttaac  putative branch site (score: 2)
                                   attgatttttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccaatgaaacccaaatctgaaccagctagcttcatgagaacaaaagctaaaaccattaagctagtcgattacctgctagattgatttttaactttacagGTTAATCGATGAAGCTTTAGGAAAGGCAGTTAAAGTTGCAGTGTGCAGTACATCAAATGAGAAAGCT

- - - - aacccaa
- - - - - - - - -ctgaacc
- - - - - - - - - - - - - - - cttcatg
- - - - - - - - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcta