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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA

Basic information

species Zea mays
transcript GRMZM2G168176_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 3
gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
||| | ||   |  ||       |||||  | || ||   || ||||      ||| |  |    ||| || ||||   | |    ||||    ||| |||||||||||||||||||||||||||||| || ||||||||||||||||||||||| ||| | ||||||||||||||||||||||| |||||||| ||| |
gtaagtatgtcaagtatttgtgagctgtaatctgtaca--agattatggacattattccatca--gtgcctaaatgtccagt---aatgtttacatgcagTTCACACCATGGAGGAGTTGAAGCTTACAGGGAACCATCTGAAAGGGTCACGGCCTCTTATAACATTTTCTACAAATTTTGATGAACAACCTCACTGGCA

upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtatgaataatacttacactgtggctgtcttatgcactccagtttataatttgtatgcttttgtcgtgacttaa-tgatt-----aatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
                                                                                            |  | ||  | |||      |     | || ||   | |  |   |   |    |  || ||  ||   || | |||||       |  |          |  ||||||||| |||||||| |||||||||||||| || || ||  | || || || ||| || | ||||||||  ||||||||||  |  |  | ||||||||
gtaatagtttcatctgattatagtcataaggttaatacaatatcatttttcttgctatgatgatttagtgttctgatttgtgtatactctaatcggcatttttcttgttggattatgattttttgtgtttctctcactctctcaactatttctgatgtacttttactgatttctgtgtttcctccactgctttccagTTCACACAATGGAGGAATTGAAGCTTACGGGAAATCACCTACAGGGTTCCCGTCCAATTTTGACATTTTCAGCAAATTTTGAAAAAGATGCACATTGGAA

upper sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G15460.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------gtatgaataatacttacactgtggctgtcttatgcactccagtttat-aatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
                                         ||| | ||   || | |    || |    |       ||||||| |||||||||  | |    ||    |     | |||  |  | || |||   ||||||||| ||||||||| |||| || || || || ||||||||||| ||||| |||||| | ||||| ||  | ||||||||  |  |  | || |||||
gtaatttgtctccagctcctcttatttggtttcaaaataagtgactgatggatataataatact-ttgggtaatgatgagtttatcaatttgtatcgtctctgagtagtgtttctgtaaatttctgtatggtga---agTTCACACAATGGAGGAGCTGAAACTCACTGGAAATCATCTGAAAGGTTCACGCCCACTTTTGACATTCTCATCCAATTTTGAAAACGATGCACACTGGAA

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|101388447|gb|EB816210.1|EB816210
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|211512372|gb|FL212647.1|FL212647
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGNAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|148943696|gb|EC888763.2|EC888763
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|76289778|gb|DV029346.1|DV029346
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|76285403|gb|DV024971.1|DV024971
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|71325419|gb|DR799392.1|DR799392
EST:     GATGGTGAAGCCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|71307148|gb|DR789745.1|DR789745
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|28930902|gb|CB334263.1|CB334263
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCT
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCT
EST: gi|89759058|gb|DY688001.1|DY688001
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|6827088|gb|AW330731.1|AW330731
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|76283913|gb|DV023481.1|DV023481
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|78180563|gb|DV550891.1|DV550891
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|32945542|gb|CF050361.1|CF050361
EST:     GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
EST: gi|18659405|gb|BM500320.1|BM500320
EST:     GATGGNGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTG                         TTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC
genomic: GATGGTGAAGTCTCCTGGAGGACCATCAGTGAAATTTCTAGTTAATGCTGgtatgaataa ... gatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatttgtatgcttttgtcgtgacttaatgattaatcacgatgtgatgatgtagTTCACACCATGGAGGAGTTGAAGCTTACGGGTAACCATCTGAAAGGGTCACGGCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAA
                              gattaat  putative branch site (score: 3)
                       acttaatgattaat  TA-rich tract