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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttctcttgccaaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA

Basic information

species Arabidopsis thaliana
transcript AT3G25040.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g30800.2 (Oryza sativa), 3'ss of exon 3
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttctcttgccaaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA
                                                     | |   || |  || || ||||     |||||      || ||  ||  ||  ||        |  || |   ||  |||     |   ||     |  | |  ||||| |  ||||| | |||||||||||||||||||  |||||| |||||||||||||| |||| ||| || |||||||
-----------------------------------------------------ttttcagattctatgcaccatta----ttctccattggaagtcagtatgttctttagttagaaatcttgacgttttcattttcgcattgat-----tgacatgatgcagCGCATACCGAGCATTATACATCCTCAACTGGGCCTACCGCTACTTCACTGAGCCACACTATGTGCATTGGATAA

upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttc-tcttgc-caaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA
                                                                |||      |||  | ||| | |||  ||   |||   |||| |         |  | | |||    | |  || |    | | |    |  |  ||||| |  |||||||   | || ||||| |||||||||||||| |||||||||||||| || || ||||| |||||||
----------------------------------------------------------------gatgttatgttggatcttcattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA

upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttctcttgccaaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttct--tgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA
                                                     | || ||   ||||   ||      | | || |||   |   |  ||||||       ||||   ||  ||||    ||| ||| | |       ||   ||    ||||| |  |||||||   | || ||||| |||||||| ||||| |||||||||||||| || ||||| ||||||||||
-----------------------------------------------------tatcatgctaggatcagtc-----ttatccttttggacagagccttaatttg-----tctctagtttatatacgct-attactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA

upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 3
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttct-cttgccaaactctataatttagtttccctctgagtttcatact-tcgattgctataccaataatg-ctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA
                                                                 || | |    |  |||||  ||      |   | |  |||  ||    || | |  |||||   |  ||   ||||  | || || ||  ||   ||||| |  ||| | ||| ||||||| |||||||||||||| || ||||| |||||||| |||||||| || |||||||
-----------------------------------------------------------------attcttataagcttgttcaactcatttgaagtttttgtttgtttgaagtccgtgaatcataaaattcatgtttataatactattgtctggctcaatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA

upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G35390.1 (Glycine max), 3'ss of exon 3
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttctcttgccaaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatg-ctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA-
                                                    ||||  |||       | |  |  |||   |  |||| |  || | |  || |  | |    ||| |   | | ||  ||   | ||  | |  || ||  ||   ||||| |  ||| | | | ||||||| ||||||||||||||||| ||||| || ||||| |||||||| || ||||||| 
---------------------------------------------------attcttatga------gcttgctcaact---catttgcaattctttttgtttgaagtccg---tgaatcataaaatt-aatgtttgtaatatttttgtctggctaaatgcagtGCATACAGAGCACTATACATTCTCAACTGGATCTACCGCTACTTTACCGAGCCTCACTTTGTCCATTGGATAAG

upper sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G46570.2 (Glycine max), 3'ss of exon 3
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttct-cttgccaaactctataatttagtttccctctgagtttcatact-tcgattgctataccaataatg-ctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA--------------------------
                                                                 || | |    |  |||||  ||      |   | |  |||  ||    || | |  |||||   |  ||   ||||  | || || ||  ||   ||||| |  ||| | ||| ||||||| |||||||||||||| || ||||| |||||||| |||||||| || |||||||                          
-----------------------------------------------------------------attcttataagcttgttcaactcatttgaagtttttgtttgtttgaagtccgtgaatcataaaattcatgtttataatactattgtctggctcaatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAGTATGATTCTCTCTTATTGTGTTTTA

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|164162086|gb|ES078190.1|ES078190
EST:     TATTGACAACTTGACCGGACAATATATATTTCTCCTTGG                         GGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
genomic: TATTGACAACTTGACCGGACAATATATATTTCTCCTTGGgtacgatctt ... cttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
EST: gi|124916597|gb|EH990471.1|EH990471
EST:     GGACTAGAAATATTGACAACTTGACCGGACTAATATATATTTCTCCTTGG                         GGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
genomic: GGACTAGAAATATTGACAACTTGACCGGAC-AATATATATTTCTCCTTGGgtacgatctt ... cttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
EST: gi|124767931|gb|EH858061.1|EH858061
EST:     AGGACTAGAAATATTGACAACTTGACCGGACAATATATATTTCTCCTT-G                         GGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
genomic: AGGACTAGAAATATTGACAACTTGACCGGACAATATATATTTCTCCTTGGgtacgatctt ... cttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
EST: gi|125198249|gb|EL213203.1|EL213203
EST:     ATATTTCTCCTT-G                         GGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA
genomic: ATATTTCTCCTTGGgtacgatctt ... cttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctctgagtttcatacttcgattgctataccaataatgctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA
                                       tgctctcttcttgc  CT-rich tract
                                  aataat  TA-rich tract