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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcatttgtaacactataataaattattaatgttgctcaatgaagaaaaaatatatcttacctggtgaactcttcttacgccttttctcccacacatacccagAGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGG

Basic information

species Zea mays
transcript GRMZM2G007871_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 4
gtacctcatttgtaacactataataaattattaatgttgctcaatgaagaaaaaatatatcttacctggtgaactcttcttacgccttttctcccacacatacccagAGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGG
        |||||  ||| ||  |  || || |||| |||| |||    || |||| || ||   ||  | |    || |||    |||  |   | || | ||||||||| || || |||||  |||||| |||||||||||||||||| || |||||||||||| |||||||||| || |||||||| ||||||||||| |||||
--gtaaagtttgtctcac-atttttgataatcaatggtgctaaat----aagaaatgtagctgggcttatta----ttattatttttttgttttgaaactttcccagAGGCCCACAAGTACTTTGTTGAATTTATATCCAAGGCATATCAGGCTTTAACTGATCCTGTATCTCGTGAAAACTATGAGAAGTATGGTCACCCAGATGG

upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S241_31V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------gtacctcatttgtaa-cactataataaattattaatgttgctcaatgaagaaaaaatatatcttacctggtgaactctt-----cttacgccttttctcccaca--------catacccagAGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGG
                                                                                |  |  | |  ||  |||  |   |  |||||  || || |    | |     | ||| ||   |      |||||||     | | | | |    ||  ||         |||   |||||||  | || |||||| | ||  | ||  | ||||||||||||||| |||| |||||| ||||  | |||||||| ||||| ||||||||||| |||||
gtgcgctcttattctgctttgtgatgtgtgtatgtgtgtgtgagtttttccctccccgtactgttagtgccattaggatctgtcgaagtcttattcacctttcgagtttattggtggtg-tgggcggaactttagtatttcccgctacactaactctttagcgcgtccacttgcaatctgacgttttcttccatgtgcagAGGCAAACAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGG
















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|71436007|gb|DR817057.1|DR817057
EST:     ATATAGGAGACTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAG                         AGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAA
genomic: ATATAGGAGACTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgtacctcatt ... acatacccagAGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatatcttacctggtgaactcttcttacgccttttctcccacacatacccagAGGCTCATAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGG
                        ttcttac  putative branch site (score: 2)
                                ccttttctcccacac  CT-rich tract
     tatctta  TA-rich tract