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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 7
gtatgttcatttttttttgatgagttcttggagatgagttat-catttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
||||| |  | || |  || |    | |||    || |||   ||| |   | |  ||| |  |||| |    | | |||||| || ||||||||||||||||| || || ||||| ||||| || ||||| || ||||| |||||||| || |||||||||||||  || ||||| || |
gtatgct--tcttgtcctgctagcatgttgattctgtgttgcacatgtatttgacaatg-cagacactc----catttcagGTTCCTGGTGAACCTAACATATCATACATTTGCTCGCGGTATTATAGGGCTCCTGAACTAATATTTGGAGCTACAGAGTATACCACAGCAATTGATATCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 7
gtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
||||  |  | | |||| | |   ||||     ||   |  ||||     |||| | |   || | || ||     |||||| || ||||| ||||||||||| || || ||||| ||||| || ||||| || ||||| |||||||| || || |||||||||| ||| || || || |
gtatacttctctcttttagtttgtttctgctgaata--tcttcatggatttaataaagtaaaatatccatt-----tcagGTCCCTGGTGAGCCTAACATATCGTACATTTGCTCGCGGTATTATAGGGCTCCTGAACTAATATTTGGAGCTACGGAGTATACCACTGCGATCGATATCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 7
gtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
|||   |   | | ||||  |  |||| ||  ||  |  | ||||     |||| | |   || | || ||     |||||| || ||||| ||||||||||| || || ||||| ||||| || ||||| || ||||| |||||||| || || |||||||||| ||| || || || |
gtacactt-ctctcttttagtttgttcctgttgaatatct-tcatggatttaataaagtaaaatatccatt-----tcagGTCCCTGGTGAGCCTAACATATCGTACATTTGCTCGCGGTATTATAGGGCTCCTGAACTAATATTTGGAGCTACGGAGTATACCACTGCAATCGATATCT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 7
------gtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
       ||| ||| |||||  ||    |  | |   || ||    ||  ||||            | | |   || | |    |||| || || ||||| |||||||| ||||||||||| ||||| || || || ||||||||||||||||| || ||||| || || | ||| ||||| || |
gtaagtttattttcgtttttccttatcaa--tttgaaagttgtacaatagtttgtgcctgagcttgtgatattatt-gtgctatagGTGCCTGGCGAACCCAACATATCGTATATATGCTCGCGGTATTATAGAGCTCCAGAACTTATATTTGGTGCAACAGAATACACAACTGCTATTGATATTT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 7
gtatgttcattt-ttttttga---tgagttcttggagatgagtt-atcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
||  |||| |||   || |||   |||  | ||| ||||   || ||  | ||      | |   | |     ||    | |||||| ||||||||||| |||||||| || || ||||| || || || || || |||||||||||||||||||| || || || || | ||| ||||| ||||
gtgagttcctttaccttctgaatttgaacttttgaagatattttgattgtatgctcctgggtttatgatcttattgcattttcagGTTCCCGGTGAACCCAACATATCGTACATTTGCTCTCGATATTATAGAGCTCCAGAACTTATATTTGGGGCAACTGAATACACAACTGCTATTGATATGT

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 7
---gtatgttcatttttttttgatgagttcttggagat-gagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT-
   || ||||  || |||||   ||     ||| |  | |    |   ||||  |         | | |   || | |  | |||| || || ||||| |||||||| || |||||||| ||||| || || || ||||||||||||||||| || ||||| || || | ||| ||||| || | 
taagtttgttttttgtttttccttgtcactttgaaagttgtacaacagtttgtgtctgagcttgtgatattatt-gtgctttaggTGCCTGGCGAACCCAACATATCGTACATATGCTCGCGGTATTATAGAGCTCCAGAACTTATATTTGGTGCAACAGAATACACAACTGCTATTGATATTTG

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 7
gtatgttcattt-ttttttga---tgagttcttggagatgagtt-atcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
||| |||| |||   || |||   |||  | ||| ||||   || ||| | ||        |   | | |   ||    | |||||| || |||||||| |||||||| || || ||||| || || || || || |||||||||||||||||||| || || || || | ||| ||||| ||||
gtaagttcctttaccttctgaatttgaacttttgaagatattttgatcgtatgctcctgcgtttatgatatgattgcattttcagGTTCCTGGTGAACCCAACATATCGTACATTTGCTCTCGATATTATAGAGCTCCAGAACTTATATTTGGGGCTACTGAATACACAATTGCTATTGATATGT

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|164172042|gb|ES040079.1|ES040079
EST:     ATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACACGGCC
genomic: ATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
EST: gi|124857013|gb|EH941450.1|EH941450
EST:     TCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTA
genomic: TCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTA
EST: gi|125116831|gb|EL166214.1|EL166214
EST:     CCAAACTCATCAATTAAAAATATGCGATTTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATAT
genomic: CCAAACTCATCAATTAAAAATATGCGATTTT-GGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATAT
EST: gi|125244903|gb|EL258988.1|EL258988
EST:     CCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATAT
genomic: CCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATAT
EST: gi|124787604|gb|EH877283.1|EH877283
EST:     GGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
genomic: GGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
EST: gi|164032470|gb|ES068755.1|ES068755
EST:     ATGCGATTTTGGAAGCGCAAAGATGTTG                         GTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC
genomic: ATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcat ... tgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcagGTACCCGGTGAACCTAACATATCCTATATATGCTCCCGGTACTACAGGGCCCCAGAACTTATATTTGGGGCGACAGAGTATACCAATGCCATTGACATGT
                                ggctaac  putative branch site (score: 2)
                                      cacccttt  CT-rich tract
             ttatcatttgaataat  TA-rich tract