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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctaacctaatgtgttgttcctgaggctactccgctgctgctgttttcctacgtcgttgtctaattcaagttccgtatgccttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG

Basic information

species Zea mays
transcript GRMZM2G477146_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
---------------gtatg-gctaacctaatgtgttgttcctgaggctactccgc-tgctgctgttttcctacgtcgttgtctaattcaagttccgtatgccttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
               | | |  ||||||||| | ||||||| |  | || ||   | |||   ||   |  ||  |  || ||||||| ||  | |        | ||| ||||||||| ||| ||||||| || |||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||
gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttc------tctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG

upper sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 10
-----------------gtatggctaacctaatgtgtt------gttcctgaggctactccgctgctgctgttttcctacgtcg----ttgtctaattcaagttccgt--atgccttatgtga-----cagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
                 |||  | |    |  || | |       ||  ||    |  |  | ||  |    |||   | ||      ||| | |||   | | |     | ||||| |   |     |||||| | ||  ||||||| || |||||||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| || |||||||||||| 
gtaaggctttttcttgggtaaagattctttgttgggctttatcaatttgtgctaatgttttgatgaggtaactttttgaagttaatttttgacaaatgtgaatgctaacgaagccttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTA

upper sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 10
------------------------------gtatggctaacctaat--gtgttgttcctgaggctactccgctgct-gctgttttcctacgtcgttgtctaattcaagttccgtatgccttatgtg-acagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
                              ||  ||||     |||  ||| || |  |  |         ||  | |  |||    || | |       ||| | |   | || |     |  ||  |||||| | ||  ||||||| || |||||||| ||||||||||| || |||||||| |||||||| ||  | ||||| |||||||| || |||||||||||| 
gtaaggctttttctttggtaaagattctttgttgggctttatcaatttgtgctgatgttttgatggggtaactttttgaagttaatttatgacaaatgtgaatgctaacccggtcttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTA

upper sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
-------gtatggctaacctaatgtgttgttcctgaggctactccgctgctgctgttttc-ctacgtcgttgtctaattcaa---gttccgtatgc-cttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
         |     || ||| ||   | ||      | | ||  | || ||| |||    |||  | |||    || | ||   ||     |||  ||| |||  |||||| ||||| ||||||| ||  ||||  ||| ||||||||| || || |||||||||||||| ||||||||||| |||||||| || ||||||||||   
gtaaaaaaaaacctcaagctactgaaatatttt----ggtgctttgttg-tgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA

upper sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 9
gtatggctaacctaatgtgttgttcctgaggctactccgctgctgctgttttcctacgtcgttgtcta-attcaagttccgtatgc---cttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
  |  |  ||   ||   |         |   | |   |||||   || ||    | ||     | |  |  ||| |    |||     ||  |    |||||||||||  |||| || ||| ||||||| ||||||||||| || |||||||| |||||||||||||||||||| |||||||||||||||||||||||||
agagagaaaaagaaaaaagaaacaaaaaaaaat-caatgctgcaattggttggacatgttaaattttgcaaacaactgatatatattatctccttctgcagATGGCAAGGTTGAACGAAGGGTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTG

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|67033412|gb|CO462161.1|CO462161
EST:     GTTCACATATTCGATCGTTCTCCTGTTTCTGTGTACTGCTGGGATTTGGG                         ATGGCA-GACTGAATGAGGGGCTGTCATTATTTGATGNCA-TACTGATTG
genomic: GTTCACATATTCGATCGTTCTCCTGTTTCTGTGTACTGCTGG-ATTTTGGgtatggctaa ... tatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATG-CAATACTGATTG
EST: gi|32847829|gb|CD987510.1|CD987510
EST:     GGTTCACATATTCCATCGTTCTCCTGTTTCTGTGTACTGCTGGATTTTGG                         ATGGCAAGACTGAATGAAGGAGCTGTCATTATTTGATGCAATACTGATTGT
genomic: GGTTCACATATTCGATCGTTCTCCTGTTTCTGTGTACTGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGCAAGACTGAATGAGGG-GCTGTCATTATTTGATGCAATACTGATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgttttcctacgtcgttgtctaattcaagttccgtatgccttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
                     gtctaat  putative branch site (score: 3)
                        taattcaa  TA-rich tract