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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcag

Basic information

species Zea mays
transcript GRMZM2G068255_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 3
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcag
|||||| |||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| || |||| |||||| ||||| |||||||||||| |         |   |  |   |||| || |||     |   |  | |  | | | |||    ||       ||||| ||||||||||    || | || |||
GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGgtttgaa--------gtacccaacttgttcaattactg-----ccattgttcagcttcgtttttgtactg-----ctaccttattacttttga----cactattgcag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 4
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcacc--ttgttactttt--gaacaacattctttcag
||||| ||||| ||| ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||  ||  | ||||| |||||||||| ||   |  |  |||  |  |   || |  |  |    || |  |   ||  | ||||||     | | | | ||     ||||||| ||  ||  |            
GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagttcag-atgggcctctcttttaagtattactctg-taatgtctaaatacatattgactattactctgcaatatctgttactcttctgactagt----------

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G36570.1 (Glycine max), 5'ss of exon 4
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatatt--ttggttgagtgttcaccttgttactttt--gaacaacattctttcag
||||| ||||| ||| ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||| ||  | ||||| |||||||||| ||   |  |  |||  |  |   || |  |  |    || |  |   ||  | ||||||   |  |    |||      ||||||| ||  ||  |            
GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATGgttagtcagttcag-atgggcctctcttttaagtattactctg-taatgtctaaatacatattgactattacgctgtaatatctgttactcttctgactagt----------

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 4
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcag
||||| ||||||||  ||||||| ||||| ||||| |||||||||||||||||| | || ||| |||| || ||||| ||  | ||||| |||||||||| |||  |     |||  || |   || |     |    ||  | |   || || ||   ||| ||   |||   |     ||  ||  | | |  ||  |||   
GTTGTCAGAGATAAACGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagttcgg-atgggcttctcttttaagcattactctgtag-tgtctaagtaca---tttagtcttgtgactagtgctttgattcagtatag-atatttta--

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctc--taatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgag---tgtt-caccttgttacttttgaacaacattctttcag---------------------------------------
||  ||||||||||| ||||||| ||||| || || ||||| |||||||| || | ||| ||| | ||||| || |||||  ||||||| |||||||||  | | ||   |  ||  |||||     |  ||||||   |        || || |   | |||| ||       ||||  |   |  |  | |  ||  ||  || || |                                        
GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGTTTCTTAAATCCTGCGGATCTAGCAGCAGCCTTAAAAGAAATGAATGgtaagcaccttgtttttagtttctgtttgatgtgttgcttcatcttgatatctcatctcactgtttttgtcagaacttgttatatgattctgttctataatcactgtcgttgaacattctgatttggtccactgatttcatatgaatacacag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 4
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtt-tgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttg-aacaacattctttcag
||||| ||||||||| |||| || ||||| |  |||||||||||||| |||||||| ||||||   || || || |||||| | || || ||||| |||  |  |||| |     ||| ||     |    || |  |  | |  | ||| | ||   | | ||  | |      ||  ||| | |  || ||  | | ||  |   
GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTATGGATTTGTTAGCTTTTCCAACCCTTTAGACCTTGCAGCAGCACTTAAGGAAATGAACGgtaatagatcttttcatggttttgtcttcttccatgttttcaagtt--tgcttgt-tgggcactatgcataa----caacaatgtaattggtgcaatgaaactcagt---

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|211002219|gb|FL464441.1|FL464441
EST:     GAGCTTTTCAAACCCTACTGATCTGTCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|78080540|gb|DV508952.1|DV508952
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|31612073|gb|CD568695.1|CD568695
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|71320385|gb|DR796941.1|DR796941
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|31612074|gb|CD568696.1|CD568696
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|13150735|gb|BG321057.1|BG321057
EST:     GAGCTTTTCAAACCCTACTGACCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|74244025|gb|DT651939.1|DT651939
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|60353545|gb|DN220518.1|DN220518
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|78083193|gb|DV511586.1|DV511586
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAGTTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|111145618|gb|EE257935.1|EE257935
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|60397448|gb|DN230264.1|DN230264
EST:     GAGCTTTTCAAACCCTACTGACCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|74235772|gb|DT643686.1|DT643686
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
EST: gi|89248698|gb|DY620484.1|DY620484
EST:     GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG                         GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG
genomic: GAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatct ... attctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATGgtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcag

- - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG