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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgccttctgccctcaccactctttcaattgcttgtacatttatgcttggaacttaaaaccattccctgacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTCATGAGGGAAGTTGCCTGGGTTATATTTGATGAGGTGCATTACATGCGGG

Basic information

species Zea mays
transcript GRMZM2G040995_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 2
gtactgccttctgccctcaccactctttcaattgcttgtacatttatgcttggaacttaa------aaccattccctgacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTCATGAGGGAAGTTGCCTGGGTTATATTTGATGAGGTGCATTACATGCGGG
     |  |  |  ||| |  | ||||| || |  |    ||| |||| |      ||        || | |   |||| |||||||||||||||||| ||||||||||| |||||||| || || ||||| || |||||||||||||| || ||| ||||||||||||| || || |||||||| |
-----gtatggtatccttatgattctttgaaatcatcc--catctatgttaaatgttttgttacttaatcttgatctgaaaatgcagGTCATGACCACGGAAATTTGGCGTAGCATGCAGTATAAAGGATCAGAAGTCATGAGGGAAGTCGCTTGGATTATATTTGATGAAGTACACTACATGCGTG

upper sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtactgccttctgccctcaccactctttcaattgcttgtac-atttatgcttggaacttaaaaccattccctgacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTCATGAGGGAAGTTGCCTGGGTTATATTTGATGAGGTGCATTACATGCGGG
    ||||    |       |||    | | |||   | || |   ||||    || |  ||||      |   ||     | ||||||||||| || || |||| ||| || ||||| || || || || ||| | ||| |||| ||||| ||| |||| ||||||||||||||||||||||| |
gtaagtaccttttaaactgttcaatgttgtctcagaagtttcttttatttgctatttgttcttagttttgtgttctt-tgtttcagGTCATGACTACGGAGATTTTGCGTAGTATGCAGTATAAAGGGTCAGAGATTATGCGGGAGGTTGCGTGGATTATTTTTGATGAGGTGCATTACATGCGTG

upper sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtactgccttctgccctcacc-actctttcaattgcttgtacatttatgcttggaacttaaaaccattccctgacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTCATGAGGGAAGTTGCCTGGGTTATATTTGATGAGGTGCATTACATGCGGG
                      || |   || |  |||     |  |||| || || || |  ||||     |||      |||  ||          | ||||| |||||||||||||| ||| | || ||||||||||||||||| ||  | ||  |||| || || ||||| || ||||||||||| ||||| ||||| |
gtaggcccagttatcatttatatatttatttttttcctatttgagcctttgaaatgtttctgtattt-----tgggttgctaaattatagttctgt--ttcagGTAATGACCACAGAAATCTGGAGAAGTATGCAATACAAGGGATCAGAAATTATACGGGAGGTGGCTTGGGTAATTTTTGATGAGGTACATTATATGCGTG

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|78087134|gb|DV515527.1|DV515527
EST:     TTGGTCTCATGACTGGGGATGTCACAATTGAGCCGAATGCCTCCTGTCTG                         GTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTC
genomic: TTGGTCTCATGACTGGGGATGTCACAATTGAGCCGAATGCCTCCTGTCTGgtactgcctt ... gacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaattgcttgtacatttatgcttggaacttaaaaccattccctgacaatgcagGTCATGACCACAGAAATTTGGCGGAGCATGCAATACAAGGGATCTGAGGTCATGAGGGAAGTTGCCTGGGTTATATTTGATGAGGTGCATTACATGCGGG
                                         ccctgac  putative branch site (score: 3)
                                       ttccctg  CT-rich tract
            tacatttat  TA-rich tract