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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG

Basic information

species Zea mays
transcript GRMZM2G165195_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 2
--------caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
        ||    ||   || ||  |   | | |     |  | || |||||  || |  ||  |||||||||||| ||  || ||    ||| ||||  ||| |||||||||||||||||||| || || ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||
gagagtttcagacattatccagtg-ccaagtttttacagttggcagagtaaggtgaagacctt--tgtactgttgat-gtgaatattt---cat-ttttatatgtcagGCTCTTGCTAAGGAACTAGTGAGGTCAAGACGTGCTGTTAATCGTCTCTATGAAAACAAGGCTCAACTAAATTCAGTATCAATGCATCTTGGAGAAATTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 3
-----caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
       |||| |  |  ||| |  | | |   ||  |||  | ||||||  |  | ||||    ||  ||  |  || |||| ||    |    ||  |   |||| ||| ||||||||||||| ||||| ||     | || || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||
ggaggtgatttgttttagctg-ttgtgtttccaaggttaaaagcataaggtcagtattttgagaaac-atttctccttaatgtgatactgtgcaatttgt---agGCACTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G21900.1 (Glycine max), 3'ss of exon 2
----caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatg-acagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
       ||| |  |  ||| |   || |   ||  | |  | ||||||  |  | ||||    ||      || |   | || ||| || | | | ||   ||||| ||||||||||||||||| ||||| ||     |||| || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||
gcagtggtttgttttatctgttgagatttaa-aggttcaaaggataaggtcagtattttgagaaac----atttttccttattgtgatatttgtgtaatttgcagGCACTTGCTAAGGAACTTGTGAGATCTAGGAAAACTGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G08510.1 (Glycine max), 3'ss of exon 2
-----caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
       |||| |  |  ||| |   || |   ||  |||  | ||||||  |  | ||||    ||  ||  || || |||| ||    |    ||  |   |||| ||||||||||||||||| ||||| ||     | || || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||
ggcggtgatttgttttatctgttgagattt-caaggttaaaagcataaggtcagtattttgagaaac-atttcttcttaatgtgatattgtgcaatttgt---agGCACTTGCTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G23570.2 (Glycine max), 3'ss of exon 3
---caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatg-acagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
   |  |  ||  | |    |      |   ||  | |  | ||||||  |  | ||||    ||      || |   | || ||| || | |   ||   ||||| ||||| ||||||||||| ||||| || |   |||| || || |||||||| ||||| || ||| | |||||| ||||||||||||||||||| | ||
aggcggtgatttgttatctgttaagatttaaaggttcaaaggataaggtcagtattttgagaaac----atttctccttattgtgatatttgtgcaatttgcagGCACTTGCCAAGGAACTTGTGAGATCTAGGCAAACTGTGAACCGCCTTTATGAAAACAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 3
-caattt--ttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
 ||| |   |||     ||  |   |  || | | |       | |   || |  |||  |   || |   |  || || || |  |  ||      |  ||| | ||||||| |||| |||| ||||| ||| |  | || || |||||| |||| |||||||||||| | |||||  |||||||||||||||| |||| ||
tcaaatcaattctcttgtggaccagttagttatagttttaacttgaaattatcctttt--ttccctttccctctttaattttcttcctcataaaatttt-cagACACTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTG

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|211495219|gb|FL000399.1|FL000399
EST:     AAAGCCATCAGGGAGGCTGCCAAGCGCAATGACATGGGATCTGCAAAG                         GCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
genomic: AAAGCCATCAGGGAGGCTGCCAAGCGCAATGACATGGGATCTGCAAAGgtagtttact ... ttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
EST: gi|76010550|gb|DT937720.1|DT937720
EST:     AATGACATGGGATCTGCAAAG                         GCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
genomic: AATGACATGGGATCTGCAAAGgtagtttact ... ttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
EST: gi|71765371|gb|DR963308.1|DR963308
EST:     CAATGACATGGGATCTGCAAAG                         GCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
genomic: CAATGACATGGGATCTGCAAAGgtagtttact ... ttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
EST: gi|211495220|gb|FL000400.1|FL000400
EST:     AGAAAGCCATCAGGGAGGCTGCCAAGCGCAATGACATGGGATCTGCAAAG                         GCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT
genomic: AGAAAGCCATCAGGGAGGCTGCCAAGCGCAATGACATGGGATCTGCAAAGgtagtttact ... ttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG
                                        tatttttc  CT-rich tract
                                ttatgacatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatttttcatcactgatcttatctgtcagaataactgaataaggctaacagtttggtgtactgttgattgttgatgttatgacatatttttcatgacagGCTCTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA