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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccttcttttagttgttgttaccatgcccttgttccaccattgctgaaaagatgtgatttaagtttggttatgtgtcgcaattccattttttagaatcgcaatacctaaatctattttttccatgacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGTAGTTGCCAGTATCCCAACTGCCGAAAAGTCAAGGGGCTATTCCGTCATG

Basic information

species Zea mays
transcript GRMZM2G139977_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 15
gtaggccttcttttagttgttgttaccatgcccttgttccaccattgctgaaaagatgtgatttaagtttg-gttatgtgtcgcaattccattttttagaatcgcaatacctaaatc--tattttttccatgacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGTAGTTGCCAGTATCCCAACTGCCGAAAAGTCAAGGGGCTATTCCGTCATG
                                         |  |||  |||||  |    | |    ||| |||   | |   |    |  ||      || | |  ||||||     | ||| || |||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| || || || |||||||| ||||||||||| || || |||||||
-----------------------------------------cttttgtggaaaaactcaattctgtcattgtgttccattttctagaaacccttcaggatatagtatcacctaatgtgatgtttctttcatgacgctgcagCTAAGGAAGATGCTTGATCTTCTGGTACATGCCTCGACATGCCGCTCTGGCAGTTGTCAATACCCAAACTGCCGGAAAGTCAAGGGACTGTTTCGTCATG

upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 15
-----------------------------------------gtaggccttcttttagttgttgttacca-tgcccttgttcca--ccattgctgaa--aagatgtgatttaagtttggttatgtgtcgcaattccattttttagaatcgcaatacctaaatctattttttccatgacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGTAGTTGCCAGTATCCCAACTGCCGAAAAGTCAAGGGGCTATTCCGTCATG
                                         ||||  | ||||  |     ||   |   | | |||| |  |  |   | ||||    |||    | ||  | || |||| ||     |  |||      |  |   | | | |  || | |   |||  |   |   ||||||| || || ||||| ||||||||||| |||||||||  |||||| |||     ||| |  |||||||||||||| ||||| |||||||||||||| ||||
gtactgtaatattcagttttttgttgttgttgttgtgcatggtagatcctcttgaaaaaactgcctcttcttctcttgctttaggcttcttctgatttgagaaaacaattgggctttgttaggtcatatagctcc-cacaatgtatctgaagtgctaaagttttcatttatctaaaatatgcagCTCAGGAAAATGCTCGATCTTCTGGTGCATGCGTCGCAATGCCGTTCTCCAGTTTGTCTATATCCCAACTGCCGCAAAGTGAAGGGGCTATTCCGACATG

upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 14
gtaggccttcttttagttgttgttaccatgcccttgttccaccattgctgaaaagatgtgatttaagtttggttatg---tgtcgcaattccattttttagaatcgcaatacctaaatctatttt-ttccatgacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGTAGTTGCCAGTATCCCAACTGCCGAAAAGTCAAGGGGCTATTCCGTCATG
                                           |    |||| |   | ||| |   | ||   |||   | | | |||   ||  | |     |  ||  ||| |   |||||  ||   |||| |||||||||||||| ||||||||||| ||||| ||||| ||   |||||| |||     ||| || ||||| ||||| || ||||| ||||| || ||||| ||||
-----------------------------------------agagaaatgaacatgggggatcttgctctgtgcatgcattattggaatattatcatctttctaca-aaggcctgacattatttggttatttgacactgcagCTAAGAAAAATGCTTGATCTACTGGTGCATGCATCTCAATGCCGTTCTCCACATTGTCAATATCCAAACTGTCGCAAAGTGAAGGGCCTTTTCCGCCATG

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|28566702|gb|CB278350.1|CB278350
EST:     CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAG                         CTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGT
genomic: CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAGgtaggccttc ... gacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGT
EST: gi|76010441|gb|DT937611.1|DT937611
EST:     CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAG                         CTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATACCGCTCTGGT
genomic: CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAGgtaggccttc ... gacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGT
EST: gi|71440180|gb|DR821230.1|DR821230
EST:     CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAG                         CTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGT
genomic: CTGACCGTGATGCTCAAAACGCAGAAGCTCGGCAAATGCGTGTCCAGCAGgtaggccttc ... gacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattccattttttagaatcgcaatacctaaatctattttttccatgacgctgcagCTAAGAAAGATGCTTGATCTTCTGGTACATGCGTCGACATGCCGCTCTGGTAGTTGCCAGTATCCCAACTGCCGAAAAGTCAAGGGGCTATTCCGTCATG
                        acctaaa  putative branch site (score: 3)
                           taaatctatttttt  TA-rich tract