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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagaactcccacgtttattacaacattatttttaatcacattgcatcttttgttttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG

Basic information

species Zea mays
transcript GRMZM2G117531_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117531_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 3'ss of exon 3
-cttagaactcccacgtttattacaacattatttttaatcacattgcatcttttgttttaatcaattatcacatcctctaagtatcttttgaaa---ataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG
  |  | |  | || ||| | || ||  ||||    ||||  | |  |   |||||||  ||| || ||   | || ||||| | || ||||||    ||  ||||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| || ||||||||||||||||  | ||      
aatagggatcctcatgttaaatataaatttata---aatcgtacta-acgatttgtttctatcgatcattttacccactaagcagctattgaaattgctactagATGGCAGATGCTGGCTACCACTGCTTTGCTCCTGATTGGATAGGATTTGGGTTCAGTGATATGCCACAGCCCGGATATGGATTCGACTACACAG------

upper sequence: GRMZM2G117531_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G03260.1 (Glycine max), 3'ss of exon 3
---cttagaactcc----cacgtttattacaacattatttttaatcacatt-gcatcttttgttttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG
    || || || |    || |||| | |  |  ||||  |||||   |||   || || |||  | || | ||||   |   ||      || | | |||     || || | ||||| || | ||||||||||||||| |||||||| |||||||| |||||||| |  |||||||| |||||||| ||  | |  | ||      
gtcatttgacctacattacatgtttttcagtatcttatgattaatactatttaaattttctgtggttattatttattttaatttc----cctcctcttaaac----agTTGTCGGATGCCGGGTTCCACTGCTTTGCACCAGACTGGATAGGATTTGGTTTCAGTGACAAACCACAACCAGGATATGGTTTTAATTACACAG------

upper sequence: GRMZM2G117531_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
cttagaactcccacgtttattacaacat-tatttttaatcacattgcatcttttgtt-ttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG
 ||   | |  ||  ||   |  |  |  ||||||| |  |  |      |  |  | ||||    |||| |  |  | ||| |  | |      | || || || | ||||| || | |||||||||||||||||||||||| |||||||| |||||||| |  ||||| || |||||||| ||  | |  | ||      
-tttatattgtcattttacctttattacatatttttcagtatgtaatgattaatactattaaatggttattatttattttaatttccctcctctta-aacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG------

upper sequence: GRMZM2G117531_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G52510.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------cttagaactcccacgtttattacaacattatttttaatcacattgcatcttttgttt-ta-atcaa---ttatcacatcctctaagtatcttttgaaa-ataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG
                                      |||       | || |  || | | || | | |  || || ||| | ||| | || || ||   | |    ||| | |  || |       ||  ||| || || |||||||||| |  || |||||||||||||||||||| ||||| || |||||||| |  || || |||||||| || ||  | |  | ||      
gtgctacactgaatcttgaatcatgtgtctatatgggaaacaattgtttctaatgaaagactcttatgatttccaatgaatcatgtgtatgtatatgaagcttgagtggatcttttgtgtgttcccaacaatgtaatagTTGTCAGATGCTGGATTTCATTGCTTTGCACCTGACTGGATAGGATTCGGATTCAGTGACAAACCGCAGCCTGGATACGGTTTTAATTACACAG------

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|71771385|gb|DR969322.1|DR969322
EST:     TTCACGGAGCTCCTACTCAGTCATTTAGTTACCGGGTGGTTATGGCTCAG                         ATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGG
genomic: TTCACGGAGCTCCTACTCAGTCATTTAGTTACCGGGTGGTTATGGCTCAGgttgcttcac ... aaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGG
EST: gi|148959535|gb|EC905510.2|EC905510
EST:     TTCACGGAGCTCCTACTCAGTCATTTAGTTACCGGGTGGTTATGGCTCAG                         ATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGG
genomic: TTCACGGAGCTCCTACTCAGTCATTTAGTTACCGGGTGGTTATGGCTCAGgttgcttcac ... aaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttttgttttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG
         ttttaat  putative branch site (score: 3)
                                taagtatcttttgaaa  TA-rich tract