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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtag

Basic information

species Zea mays
transcript GRMZM2G038848_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 5'ss of exon 9
GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt---------------atttgagatta-----atcgattcatt--ttatatatctgtttcaacatcaaatga--tttggtctctaaaacatgcatcattgtag
||||||||||||||||| | ||||||||| ||||||||||||||||| ||  |||| |||||   |||  |                | |   | ||     |   ||| | |  || ||||||||     |   | | | |   ||  |||||||  |||||||   |||||
GCAAAACTGATCAAGCTGAGCAACATTATCATTGATGCAAAATCTGGGGTTTGTGGAGCAGgcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 5'ss of exon 9
GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt-atttgagat-------taatcgattcattttatatatctgtttcaacat---caaatgatttggtctcta---aaacatgcatcattgtag------------------------------------
||||||||||||||  | | ||||||||| ||||||||||||||||| || ||||| ||||||  | ||||    ||||||         ||  | | ||| ||||||| | | |  | ||    | ||   |   | | ||   | | ||    |||  |                                      
GCAAAACTGATCAAAGTGAGCAACATTATCATTGATGCAAAATCTGGGGTTAGTGGGGCAGgtatgcattttgcatgagatactctgactattaagtaattatatatatatatatatatatatatatatatatatatatatatatatatatatgccatcattattagctgatatgctgtgtaacacatgtattttgtag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 5'ss of exon 8
GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtatttatt------tgagattaatc--gattcat-----tttatatatctgtttcaacatcaaatg-attt----ggtctctaaaacatgcatcattgtag--
|| || || ||  |   ||  ||  | |||||||||||||||||||| || ||||| ||||||| | |||| ||      |    |||||    |||| |     | |||||   || ||| || |  |    ||||     |  | |   |  ||   |||| |    
GCTAATCTCATTGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAGgttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 9
lower sequence: PP1S101_184V6.1 (Physcomitrella patens), 5'ss of exon 8
GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtat----ttatttga---gattaatcgattcatt-ttatatatctgtttcaacatcaaatgatttg-gtctctaaaacatgcatcattgtag------------------------------
||   | | ||  ||      |||||||| ||| |||| || ||||||||||||||||||||| | ||     |||||||      ||  | | |||     |  |||| |  ||||     ||    | || |  | ||   |||    || |                                  
GCCGGATTAATTGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataacatattatttgctttagttcgtagtttcccaactggatattttattcacgtgtaatcagtgtgagagtttagtgcatatgacactagcacttaatgtattggaattttgtcatgtatag

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|74234670|gb|DT642584.1|DT642584
EST:     CAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
genomic: CAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGT-GGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAG-GGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtag

- - - - -  CAAGCT