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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagcctcgattgctgagaaggagagaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA

Basic information

species Zea mays
transcript GRMZM2G161337_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g15780.2 (Oryza sativa), 3'ss of exon 2
----gtgagcagcctcgattgctgagaaggaga------gaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtct-tctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA---------------------------------
    |  | |    || |    |  |||| |||      ||| ||||||| |||  | | |||  |||||||   |  | |||||| | | ||||  |||||||||||||||| |||||||||||||||||||| ||  | |||||||| ||||||||||| || |||||| ||||||| |||||||||||||||||||||||                                 
gtgagctaacgaaatcaaacagtaggaagaagaaatggggaatatttgattttgttggttatgaaatgtgaaccatggcatttggtttctttgtttgtgataggtggatgggtcgggttcttttcctatgatacagTCCGTTATGTTGAAAAGAAGAAGCTGCCCTTCTCCGGTGCTCCCCAGGACGATAGGAACCTTCCTGATGTTCACCTTGGGCTTTATGATGATGTTCTCGT

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 2
----gtgagcagcctcgattgctgagaaggaga------gaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtct-tctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
    |  | |    || |    |  |||| |||      ||| ||||||| |||  | | |||  |||||||   |  | |||||| | | ||||  |||||||||||||||| |||||||||||||||||||| ||  | |||||||| ||||||||||| || |||||| ||||||| |||||||||||||||||||||||
gtgagctaacgaaatcaaacagtaggaagaagaaatggggaatatttgattttgttggttatgaaatgtgaaccatggcatttggtttctttgtttgtgatagGTGGATGGGTCGGGTTCTTTTCCTATGATACAGTCCGTTATGTTGAAAAGAAGAAGCTGCCCTTCTCCGGTGCTCCCCAGGACGATAGGAACCTTCCTGA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT2G29690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagcagcctcgattgctgagaaggagagaagatttgatgttgccgatgatg--ttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
|||||  |       || |   ||  ||||     ||  | ||  |  || ||  || | || || ||   ||| | |      || |    |||||| |||||||| | |||||| ||||| || ||  | |||||||||||||||||||| || || || | ||||||  |||| |||||||  ||||||||
gtgagtggagaaatctgtttttaaatagagtgatgtttgttttagcattgctgatttgtttggatggttgattt-gat------ttgtaaccagGTGGTTGGGTTGGATACTTTTCATATGACACTGTACGTTATGTTGAGAAGAAGAAGCTGCCTTTTTCTAATGCTCCAGAGGATGATAGGAGTCTTCCTGA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g00400.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgagcagcctcgattgctgagaaggagagaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
        ||| |     |   ||  ||       ||  |    || |       |       |  |  ||  | | |  |   || | ||| |  ||||||||||||||||| || || || |||||||||||| | ||||| |||||||| ||||| || ||||| |  || |   | || || || || ||  | ||
agagatatgtgggttatgttccttattgtattcttgatcaatactggttcctttaaaatatgaaaatccatgcttagtaattaactaccgttttaaatagGTGGATGGGTTGGTTTTTTCTCATATGATACGGTTTGTTATGTGGAGAAGAAAAAGCTGCCATTCTCAAAAGCACAAGATGATGACAGAAATCTCGCAGA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S77_252V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtgagcagcctcgattgctg-agaaggagagaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttct--tgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
       ||   || |    |    | ||     |   |  |    | |    ||  |||   ||  ||||   | ||   |||||      |  |  |||||||||||||||| | |||||| ||||| || || |||||||| ||||| ||||||||| | || ||    || ||  | || ||  |    || |||||
tgttctttgtataggcagagtcttagcagtttatgtttaagtccagtatatttgagcatgagctg-aaatatgtagttgatgtctttgagcatgattgtagGTGGATGGGTTGGTTACTTTTCGTATGACACAGTAAGGTATGTGGAGAAAAAGAAGCTAGCCTTTTCATCAGCACCCAAAGATGACCGAGGTCTACCTGA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S154_79V6.1 (Physcomitrella patens), 3'ss of exon 4
---gtgagcagcctcgattgctgagaagg---agagaagatttg-atgttgccgatgatgttatgtgaatagtcacttttggtcttctgttcttgat--agGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
      |  | |   || |  | | |      | | || ||||| |  || |  |  |||   ||  |||  | | ||    |||||     | | |  ||| ||||||||||||| |||||| ||||| || || |||||||| ||||| |||||| | || || ||    || |||   || ||  |     | |||||
gattacataaacgctgagtcgtaacatctcctatataacatttgcacattcctaagcatgagctg-aaatttttagttgatatcttcgagcatggttgcagGAGGATGGGTTGGGTACTTTTCATATGACACTGTGAGGTATGTGGAGAAAAAGAAGTTGCCCTTTTCTTCAGCACCTATAGATGACCGAGGTTTACCTGA

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|148939627|gb|EC884266.2|EC884266
EST:     GGAGGGATGGCACCCACAGCAGATCGACGAGCTCCCTGAATCCTTCTCCG                         GTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGA
genomic: GGAGGGATGGCACCCACAGCAGATCGACGAGCTCCCTGAATCCTTCTCCGgtgagcagcc ... ttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA
 atttgat  putative branch site (score: 5)
                                      tcttctgttctt  putative PPT
             atgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagcctcgattgctgagaaggagagaagatttgatgttgccgatgatgttatgtgaatagtcacttttggtcttctgttcttgatagGTGGATGGGTTGGGTTCTTTTCCTATGATACGGTTAGGTATGTTGAGAAGAAGAAGCTACCGTTCTCCAGTGCTCCTCAGGACGATAGGAACCTTCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC