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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacttaaacagtgctctttttttggatgagcatgggtcttagaaggttctttagttctactggatataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT

Basic information

species Zea mays
transcript GRMZM2G109429_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109429_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g66960.1 (Oryza sativa), 3'ss of exon 2
agacttaaacagtgctctttttttggatgagcatgggtcttagaa---ggttctttagttctactggatataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT
       |    | |    |     | ||| | |  ||||||  |    |    ||  ||| | ||||| ||| |  | |    |  |||||  || || ||||||||||| ||||||||||||||||||||||||||||| || || || |||||||||||| | || |||||||||||||| ||||||||||||||||| |
--ggccgagttttccaagctgaagtgctgaacttcagtcttaccacatagcagcttgcttccattggatttaa-acataatacctgtctgttttctattgcagCTCACATTCTCTGGTGCAATTATTGAGGTGTGCATGAGAAAGCTTGTGTTTTATCCAGAAATCGTGGGCTTCCTCGAAGAGGATAAAGACGACTTCCCTT

upper sequence: GRMZM2G109429_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G15540.1 (Glycine max), 3'ss of exon 2
------agacttaaacagtgctc------tttttttggatgagcatgggtcttagaaggttctttagttctactggatataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT
      | | || |||| | | |      |    |   |  | ||     |  ||||       |||       | |   ||||||  | |  ||  | ||  |  ||| || | || |  ||||| ||  |  | || || |||||||||||||| || || ||||| ||||||||||||||  | ||||| || |||||  | || ||||
tttatgacatttcaacattccaccacatatcccctctcaccaacacaca-cacagaaaagatgatag-------gaaggcaacatc--attaattctttttaac--ttttagATTACGTACTCTGGAGCTTTGCTGGAAGTCTGCATGAGGAAACTTGTTTTCTATCCTGAAGTTGTTGGCTTTATTGAAGATGAAAAAGATCAATTTCCAT

upper sequence: GRMZM2G109429_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 2
agacttaaacagtgctctttttttggatgag--catgggtcttagaaggttctttagttctactgga-tataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT
 |  |   |   |  |  | |||| | |||   ||| |  || |    ||||| |   |  |||||| |     ||||     | || |||   ||  | ||| | || | ||| ||||||||  | ||||||||||||||||||||||| || ||||| ||||||||||| ||  | |||||||| || ||  | ||||| |
-gtttgctattctcatggtattttagttgatttcattgtactaaccttgttctatttgtagactggagtgctttatctataactctgatgt--gctactgcagATTACCTATTCCGGTGCAATACTGGAGGTGTGCATGAGGAAACTGGTTTTCTATCCCGAAGTTGTTGGTTTTATTGAAGAAGAGAAGGATAAATTCCCTT

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|211452461|gb|FL410333.1|FL410333
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211390309|gb|FL404115.1|FL404115
EST:     AGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|91056504|gb|EB166922.1|EB166922
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211264276|gb|FL294960.1|FL294960
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211173040|gb|FL404342.1|FL404342
EST:     AGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211425792|gb|FL370218.1|FL370218
EST:     AGGATTGCCGTAAATKTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|13558509|gb|BG549865.1|BG549865
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211108328|gb|FL388568.1|FL388568
EST:     AGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211264271|gb|FL294955.1|FL294955
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211003072|gb|FL395292.1|FL395292
EST:     AGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|13558052|gb|BG549408.1|BG549408
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
EST: gi|211116346|gb|FL427489.1|FL427489
EST:     AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG                         CTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT
genomic: AGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAGgtattaacta ... cctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctttagttctactggatataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT
                          atctgac  putative branch site (score: 3)
                                             cctgtttc  putative PPT
                   atataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacttaaacagtgctctttttttggatgagcatgggtcttagaaggttctttagttctactggatataacatctgactgtttgctgttgcctgtttcagCTCACATTTTCTGGTGCAATTATTGAGGTGTGCATGAGGAAACTGGTATTTTATCCAGAAGTTGTTGGCTTCCTCGAAGAAGATAAAGACGACTTCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG