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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttgctgcctataatggtttatgtctgttactctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc...

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 5'ss of exon 4
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctt-tgctgcctataatggtttatgtctgtt-----actctgttccttaaatgcttttgtgtctctacttca-taaaaacccaacctataatgcatttttcc
|||||||||||||| || ||||||||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||||||||||||||| | || | ||| |  | | || | ||||||     | | | ||| |    | |||     |    | || |  |       ||    |||   | ||    
GACATATGGAAGATTCGCCTTCAACTTACTAAGCCAGTGACATGGCCTCCGCTTGTATGGGGAGTGCTTTGTGGAGCAGCTGCCTCTGgtatgcctatggtacctttcgttgattttatctgtttggagagtttattcttc---tacttcctaataatcatttgagcacctgtagaattggtaaactactt----

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 4
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtat---gctttgctgcctataatgg--tttatgtctgttactc-tgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc
 | |  |||||||| |||||||||||||| ||||| || || ||||||||  | |||||||| ||  | |||||||| ||||| |||||||      | |      ||  ||    || |  | ||  |  | || ||   |||    || ||    |   ||| |   |    ||    | |  ||| ||   
AATAAGTGGAAGATTCGTCTTCAACTTACAAAGCCAGTCACTTGGCCTCCATTAGTTTGGGGTGTAGTTTGTGGAGCTGCTGCTTCTGgtactaaattctatcaattagcataacattaaaatgtgacatgcatggtcacaaaaaaaattggtcctgcatgttcctgtga---taattgtttacacatgtt---

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 4
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtat---gctttgctgcctataatg--gtttatgtctgttactctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc
 | | ||||||||| ||||||||||| || ||||| || || ||||||||| | |||||||| ||  | ||||| || |||||||| ||||      | |     |||  ||   ||| |    ||  |  |  || |  |||    ||||   ||  |  |  |||      ||    | |  ||| ||   
AATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaattctatcaactagcataatgttaaaacttgacatgcattttcacaaaaatgtttggtccttcatat--taatgtgataattgtttacacatgtt---

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G19340.1 (Glycine max), 5'ss of exon 1
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtat---gctttgctgcctataatg--gtttatgtctgttactctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc
 | | ||||||||| ||||||||||| || ||||| || || ||||||||| | |||||||||||  | ||||| || |||||||| ||||      | |     |||  ||   ||| |    ||  |  |  || |   ||    |||| ||| || | |  |||      ||    | |  ||| ||   
AATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGAGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaattctatcaactagcataatgttaaaacttgacatgcattttcactaaaatgtttg-gtc-ctgcatattaatgtgataattgtttacacatgtt---

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 5'ss of exon 4
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttgctgcctataatggtttatgtctgttactctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc
 | | ||||||||| |||||||| ||||| || || || || |||||||| || |||||||||||  ||||||| || ||||| || ||||  | |     ||| |  ||| | |||      |  |||| |   || |  |||  |   | | ||||  |      |  |    |            
AATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAGgtaatcatacgaacctcttttggatcatgca----atactgtacagaaagttttttcat---tttccttccaattgtttcttctggcag-----------

upper sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 4
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgta---tgctttgctgcctataatggtttatgtctgtta-ctctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc
 | | ||||||||| |||||||||||||| ||||| || || ||||| ||| | |||||||||||  | |||||||| ||||| |||||||   |||||   |   |||| ||    ||   | ||| |||||  ||   ||   || ||     |   ||       ||      | |  |  || |||| 
AATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTGgtactctgcttatatatatatattgtggaattaatattatctctggccc---aacatttatgctgaacatttttgctcttacttggaatttgttaaatctttc-

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|149038823|gb|EE155536.2|EE155536
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|211379068|gb|FL028409.1|FL028409
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|211302748|gb|FL028408.1|FL028408
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|61119511|gb|DN560472.1|DN560472
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|211379069|gb|FL028410.1|FL028410
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGACCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
EST: gi|149080582|gb|EE169625.2|EE169625
EST:     GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG                         GAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA
genomic: GACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttg ... tctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTGgtatgctttgctgcctataatggtttatgtctgttactctgttccttaaatgcttttgtgtctctacttcataaaaacccaacctataatgcatttttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC