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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG

Basic information

species Arabidopsis thaliana
transcript AT1G49240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
--gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatg-attttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
   |  || |||| |  |       |||     |   ||    ||   | | || | || | || |      || | |||||   ||    || |  |||||||||| | || ||||||||||||||| ||||||| ||||| ||||| || || |   ||||||| |||||||| || ||  | || |||||||||||
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatat------gaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctt-tagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
                    |  | ||   ||  |    || ||     ||||||  | ||| |||  ||  |||        || | ||  |  |||||| |||||||||||||||||||||||    ||||| ||||| ||||| || || |   | ||||| ||||| ||||| ||||| ||||||||||| ||
--------------------gtaataactcactca--catggttgagagttttaaaaaatat-tcactttattcatgaactgttgctcttgatgcagGTATCGTGTTGGACTCTGGTGATGGTGTCAGCCACACCGTGCCAATCTATGAAGGATATGCCCTTCCTCATGCCATCCTGCGTCTGGACCTTGCTGGGCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
         | || | | |  |  |     || || |||  ||     ||   ||  ||| |  ||| |  || |  |     ||  || ||| ||||||||||||||||||||||||||||||    ||||| ||||| |||||||| ||||   | ||||| ||||| ||||| ||||| ||||||||||| ||
--------gtaatgattctttaacatggtgaccaaatttcattaggacttcccaa--atttttccatctcaattatggattgctg--ttccttcagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACCGTGCCAATCTACGAAGGTTATGCCCTTCCTCATGCCATCCTGCGTCTTGACCTTGCTGGGCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G437445_T01 (Zea mays), 3'ss of exon 4
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatga--ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
                      |  | || |  || | | ||||  | |    |    | |  | ||| ||    |||||| | ||   |||||  |||||||||| | ||||||||||||||||||   ||||| || ||||||||||| || | | | ||||| |||||||| || ||  | ||||||||||||| 
------------------gtatgttactgcattaaatct-gtttcatatc---agcattcaaataatagtgtagtcagtgataggaatctttctgcagGTATTGTGCTCGACTCTGGTGATGGTGTGAGCCACACCGTCCCTATCTACGAAGGGTACACGCTTCCTCATGCTATTCTTCGATTGGACCTTGCTGGTCA

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G053299_T01 (Zea mays), 3'ss of exon 3
------------gttagttcattattaatgtcgagaaaatgaacaaagt-tttgttttctgtttttaatgatt-----atgtcatattgatcacagtgaaatgattttcttt----agGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
             ||      ||||||| ||      |  | |||| || | || ||   ||  ||  ||||      |   |||  |  |  |  ||    | |  ||| |    |||||||||| | || ||||||||||||||| | ||||| ||||| ||||||||||| | | | || || ||||| || ||  | || || |||||||| ||
gcacgtgtccactttcacctcttattaaagtttttcta--ggacaacgtctctgattctcgtcattggtgatctgacgacaccattctactacctatgtctcggtactctgtgtgcagGTATTGTGCTCGATTCTGGTGATGGTGTGACCCACACCGTGCCAATCTACGAGGGATACGCGCTCCCTCATGCCATTCTTAGGCTGGATCTTGCTGGCCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttc-tttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
      | || | |   ||  | |    || |||| |||  ||    |   |||   ||| |  ||| || || |  |     || |  || || ||||||||| ||||||||||||||||||||    ||||| ||||| ||||| || ||||   | ||||| ||||| ||||| || || ||||||||||| ||
-----gtaatgact--cgttcacatggcgaccaaa-tttcatta---ggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G110378_T03 (Zea mays), 3'ss of exon 4
-----------gttagttcattattaatgtcgagaaaatgaacaaagt--tttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
             ||  ||| || |||      |||  | |||| | |  |||   |  |||   | ||| ||  |   | ||  |  |  | ||       |||  |||||||||  | ||||||||||||||||||  |||||||||||| || || || || |   | ||||| ||||| || || ||||| || |||||||||||
aaaataagcataatacatcaataataaacaatggaagttaaacataattgtttacatggtgtggctgatgtttccgcttttttattttc--tcaa-------tctacagGTATTGTTCTCGACTCTGGTGATGGTGTGAGTCACACTGTGCCCATTTATGAAGGATATGCCCTTCCCCATGCCATTCTTCGTCTGGATCTTGCTGGTCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgttttta-atgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
    |||  |  ||| |  |     |     |  | ||   |  | ||| || | ||  || | || | |  ||||     ||    |||   | ||||||||| |||||||||||||||||||||  |||||||||||| ||||| ||||| |   |||| || ||||| || |||||| | || |||||||| ||
----gtttgtacttatttcc-----atctgtcttaattcactcctttgtcttcacattgttctatcct-tgaatca-----aatctttttgaatcagGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctt--tagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
                 ||    | | |       || ||| ||  |  ||||| | || |  ||||  |   |       |||   ||||     |||||||||||||||||||||||||||||||  ||||||||| || ||||| ||||| |   |||| || ||||| ||||| ||| | || || || |||||
-----------------gtttgtatattaccatctgtcttgattcattctttta-taatcacatcattctttccctgaatcaattcctttcaaaacagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctt--tagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
                 ||    | |         || ||| ||  |  ||||| | || |  |  |  |   |       |||   |||      ||||||||| |||||||||||||||||||||  ||||||||| || ||||| ||||| |   |||| || ||||| ||||| ||| | || || ||||||||
-----------------gtttgtatatcaccatctgtcttgattcattctttta-taatcacattgttctttccctgaatcaattccttttaaaacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttct---ttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
    |||  | |||  | || |             ||||   ||  |  ||||  | || |  |  |  |   |       ||  | |||||     ||||||||| ||||||||||| ||||||||   |||||||||||| ||||| ||||| |   |||| || ||||| || || ||| | || |||||||| ||
----gtttgt-atttgtatccatct----------gtttcaattcatagttttg-tcatcacattgttctttccctgaatcaaatactttctgaaacagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
    |||| | |||||  ||        ||    | ||||  ||| | ||||   |  |||    |   |||   |           |||   ||||||||||| |||| |||||||||||||||  |||||||||||| || || || ||||   ||||||| ||||||||||| ||||| ||||||||||| ||
----gttcgt-attaaaatctttttg--gattggaattttcatttttcttttctgttgttagtgtagcctgagttctaacttgctcctttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

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|124753824|gb|EH843954.1|EH843954
EST:     ACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: ACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|125078131|gb|EL140637.1|EL140637
EST:     CCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: CCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|47831799|gb|CK121483.1|CK121483
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|124736018|gb|EH827420.1|EH827420
EST:     GCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: GCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|86042720|gb|DR338475.1|DR338475
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|125046685|gb|EL118954.1|EL118954
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGG
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGG
EST: gi|86042713|gb|DR338468.1|DR338468
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|86042712|gb|DR338467.1|DR338467
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACG
EST: gi|124838616|gb|EH923055.1|EH923055
EST:     TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCG                         GTATTGTGTTGGACTCTGGTGATGGT
genomic: TGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcat ... ttttctttagGTATTGTGTTGGACTCTGGTGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG
                         tattgat  putative branch site (score: 3)
                                             ttttcttt  putative PPT
       tttttaatgattatgt  TA-rich tract