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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA

Basic information

species Zea mays
transcript GRMZM2G126821_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126821_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 3'ss of exon 2
gtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaat--tgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA
||||| |  ||  |  | |||  ||   |      || |||| | |    | ||||   || ||  ||| ||  ||||||  ||     ||| |||||||||| ||||||||||||||||| |||||||| ||||||||||||||||| || || || || |||||||||||||||||||||||||| || |||||||
gtgaaaatgatcaccatgtcacggtagtgcg----ttggtgaattggg--tacagt---attgtttactgatcgtgttatcctgaattatgtctgcagCCAATCAAGGAGTCTGCTCTGGGAAACATCCCGACCATTGCCTTCTGTGACACCGATTCCCCAATGCGGTATGTCGATATCGGCATCCCGGCCAACAACA

upper sequence: GRMZM2G126821_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G01460.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------gtgaacagaatttcagtttcaaagttcagaaatatttagtg-agtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA
                                                               ||  |||  ||||  |||    |  |         ||  ||  |||    |||   |||| || | |  |   |||| || | ||  |||| ||||||| ||||||||  ||||||| ||||| || ||||||||||| |||||||| ||||| || || ||| ||||||| || || || || || || |||||||
gtggatacccaaatcagcttcaaatgatatatttgattttagttacttgtgctttgattgattgttgacatgatttatgttatgtatgttgtttgcggttgttgtggtgttgactgtgttgtgttgttaatgtgtgtgtt-tgttcgt--ttgtgtgcagCCTATTAAGGAAGCTGCTCTTGGGAATATTCCCACCATTGCTTTCTGTGACACTGATTCGCCTATGAGGTATGTGGACATTGGAATTCCTGCCAACAACA

upper sequence: GRMZM2G126821_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G04890.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------gtgaacagaattt-cagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA
                                                                                ||  |   | |||   || | |  |||     |   ||  ||  | |  || |   |||| || | |  ||  |||| || ||||  |||| ||||||| ||||||||  ||||||| ||||| || ||||||||||| |||||||| || || || || ||| |||| || || || || || || || |||||||
gttagtaccctattttcatatgcagttatatgaagaaaaaaagatacatttgattctagtcacatgtggtttgattgattgttgatgtagtttatggtgtgattgtttgtttagggttgttgtattg--cccgtgttgtgttgttaatgta--tgtt-tgttggt--ttgtgtgcagCCTATTAAGGAAGCTGCTCTTGGGAATATTCCCACCATTGCTTTCTGTGACACCGATTCACCTATGAGGTACGTGGACATTGGAATTCCTGCCAACAACA

upper sequence: GRMZM2G126821_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 3'ss of exon 2
-------gtgaacagaatttcagttt-caaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA
       ||  |   |||||   |||  | |||  |  | | | |  |   ||     |  |||     ||     || || | ||     | | ||||| ||||| ||||||||  |||| || || ||||| || || ||||| |||||||| ||||| || || ||||||||||| || || || |||||||| || ||||
tattttggttcatctaatttatctttgtatagtgtatgagtttgtgtt--atgagttatttagtcca--ggatttttacttatcatcacaataactgttttcagCCTATTAAGGAAGCTGCACTAGGAAACATTCCAACTATTGCTTTCTGTGACACTGATTCCCCAATGCGGTATGTTGACATTGGTATCCCAGCCAATAACA

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|33101681|gb|CF061641.1|CF061641
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACCATCCCCACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAAC-ATCCCCACCATTGCCTTCTGTGA
EST: gi|30306590|gb|CD001263.1|CD001263
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|32850981|gb|CD990662.1|CD990662
EST:     TCAGCGAGCCTCGACTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACCATCCCCACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAAC-ATCCCCACCATTGCCTTCTGTGA
EST: gi|211540690|gb|FL218505.1|FL218505
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|18964153|gb|BM660841.1|BM660841
EST:     TCAGCGAGCCTCGACTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|28987078|gb|CB351453.1|CB351453
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|24768430|gb|CA403559.1|CA403559
EST:     GCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: GCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|7216530|gb|AW562652.1|AW562652
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|21330457|gb|BQ485838.1|BQ485838
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|31353712|gb|CD438069.1|CD438069
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGATACTGACTCTCCCATGCGGTATGTCGATATCGGCATCCCAGCGAACAACA
                        aactaat  putative branch site (score: 2)
                           taattgttat  TA-rich tract