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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC

Basic information

species Zea mays
transcript GRMZM2G155123_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g03430.3 (Oryza sativa), 3'ss of exon 8
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttat----ttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
   |||  || |   ||    |  || |||  |||   |||||||   ||  |||  ||    | |||||     ||||||  | |||| ||     | |||||||||| ||||||||||||||||||||||| || |||||||||||  |||||||||| |||||||||||||||||||| ||||||||||||||||| || |
-atataggttctaatgtcatgtcaagatgt-gtgtaaggctaagcctttcttgtg--atgcaaaattggagactaatctaatttgttttctaacatgtcttcagAATAGTGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCC

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G29270.1 (Glycine max), 3'ss of exon 9
agcatatcttttctg-gttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttattttt-cagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
 | |   ||||  ||  ||||  ||   | |  |  | |  |    |  |      || ||  | |  ||   |  || | | |   || | |  |||  |||  || || || ||||||| |||||| ||||| ||||| |||||||||||||| || |||||||||||||||  |||||||||| ||||| |||| ||| 
-gtaaggctttcatgtattgg--attattttagtactca--tggagttttataaatcagtt--cctgaggtcataaattttatacgcttgtgaaatttatagATGAGTGGTTCAAGAATGAAGATTGCAGGAAGATTCAAACCTTGTGTTCACATTGGTTGTTTTGATCTTGAAGTTTTTGTGGAAATGAATGAACGGTCAA

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatt----tttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
                     ||| ||| ||||   ||| | |  |  |   |       || | |   | |  |   |    |||||||  |     ||| |||  || || || ||||||| |||||||||||| || || || ||| |||||||||| || ||||||||||||   ||||||||| |||| ||||| ||| 
--------------------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G40320.1 (Glycine max), 3'ss of exon 9
agcatatcttttctggttggctatagctgtcatg---tttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
    ||    ||   |     | |||   |||||   |||    || | | ||| |   || |   |     |||| |||   |||  || |  | |||  |||  || || || ||||||| |||||| ||||| ||||| ||||||||||||||||| |||||||||||||||  |||||||||| ||||| |||| ||| 
---gtaaggctttcagacacttttagtactcatggagttttataaatcagttcctg---aagtcata----aaattttat---acac-ttgtgaaatttatagATGAGTGGTTCAAGAATGAAGATTGCAGGAAGATTCAAACCTTGTGTTCACATGGGTTGTTTTGATCTTGAAGTTTTTGTGGAAATGAATGAACGGTCAA

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G15880.1 (Glycine max), 3'ss of exon 13
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatt-----tttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
                     ||| ||| ||||   ||| | |  |  |   |       || | |     |  |   |    | ||||||  |     ||| |||  || || || ||||||| |||||||||||| || || || ||| |||||||||| || ||||||||||||  |||||||||| ||||||| || ||| 
--------------------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctcctaatcagtttttttttttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTTTTTGTGGAAATGAATCAGCGATCAA

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT5G60410.4 (Arabidopsis thaliana), 3'ss of exon 13
agcatatcttttctggttggctat--agctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatttt-----tcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
 | |  |   |  | | | |      || | | ||  ||| |    || |   ||   |  |||||    ||||| | | ||   | |||| | |||      | |||  ||||| || || || |   ||||||| || ||    || ||||| ||||||||||||||||| |||||    |||||||| ||||||||||| ||  
-gtaagttactaatagctcgtagcccagtttttatacttatcc--tcttcctagggctatcttgcagactgaattttttttattgtcttttctgtttgcgtcattagATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCACATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCA

upper sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 3'ss of exon 12
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttg----catttggaattgtat---ctaacatattttt-tatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
         ||| || |     | | |    |  ||| | |    ||||    || ||  ||    | ||||||||  |||    | ||  ||   | ||  || ||||  || || || ||||||| | |||||||||| ||||| ||||||| |||||||||||||||||||||||||| |||||||||| |||| ||||| ||  
--------gtttttgatgcagaaaacccaataacttttgttgcaatgcttttatgtaacctgattacttttggaatcatatatttttactcatacatgtaaattacagATGAGTGGTTCAAGAATGAAGGTTGCTGGAAGATTCAAACCTTGTGCTCACATGGGCTGTTTTGATCTTGAAATTTTTGTGGAAATGAACCAACGTTCTA

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|30306927|gb|CD001600.1|CD001600
EST:     GCGACCTGGAAGTGGTTACTGAATCTGTTACAGTCAACCTTCGTTGCCCT                         AATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCAC
genomic: GCGACCTGGAAGTGGTTACTGAATCTGTTACAGTCAACCTTCGTTGCCCTgtgcgtcttg ... tatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCAC
EST: gi|211212018|gb|FL385215.1|FL385215
EST:     GCGACCTGGAAGTGGGTACTGAATCTGTTACAGTCAACCTTCGTTGCCCT                         AATAGCGGATCCAGAATGAGGATTGCTGGAAGGGTCAAGCCTTGTGTTCAC
genomic: GCGACCTGGAAGTGGTTACTGAATCTGTTACAGTCAACCTTCGTTGCCCTgtgcgtcttg ... tatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctccggtgcaatttgcatttggaattgtatctaacatattttttatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
                              atctaac  putative branch site (score: 2)
                                      tattttttatttttc  CT-rich tract
                  atttggaattgtatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatttttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - ttttctg
- - - - - - - - - - - - -gctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcatt