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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------------------gtgattactcgattaattcttct--tacagtggtgatagtcatttgaatacatgtgttg-ctgattgctttcttttcct----gttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                                                                          ||| | |  |  | ||| ||     ||| ||  |     || |||   |||     |   || |||  | | |  |  |    | |  |||||||| ||||||||  | ||||| || |||||||| ||||| |||||||||||||| |||||||| ||||| || ||||| || ||||||||||||||||
gtttgtacagaacctaccatggttctcactcataataatatgtgcttttcctccccatttttattaaggtttctgtgttgaaccactaaatgctcaaagtactgttttccccctcttttttctactcaactaatctaattcttatatacttttaaacgatcccagCGTGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
--------------------------------------gtgatt--actcg-attaattcttcttacagtggtgata----gtcatttgaatacatgtgttgctgattgctttcttttc----ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                                      || |||  | | |  | ||   ||  |  |||| || |     ||| | |     ||| | |||| |  |    | |  |     ||||| ||||||||| |||||||| || || || || |||||||| ||||| ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||| |
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcc---tgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                                                             |  ||| | | |  |  | |||  |   || |     |||| | | |  ||          |    ||   || |   || |  |||||||| || ||||| || ||||| || ||||| || || || ||||| ||||| || || ||||||||||| |||||||| || ||||||||||||||||
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgc-caagca--ttttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
---------------------------------------------------------gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctga----ttgctttcttttcc-tgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                                                          |||   | | |   ||| |||  ||  || |     | || | | | |||    |  |||    |||  | ||||    || | ||||||||| || ||||| || ||||| || ||||| || || || ||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||||||
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcatt-ttcagacgatgtttccctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
gtgattactcgattaattcttcttacagtggtgatagtc--atttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
|| |  ||||  ||  | |    |         ||  ||  |||   |||    |  |||| | ||  |||| ||    ||  |||||||||||||||||||||||||| || |||||||| || || ||||||||||||||||||||||| ||||| ||||| || || |||||||| ||||| |
gtaa--actcagttgttaccaagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttt---tttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
|| |  ||||  ||  |      |         ||| ||   |    | | |  ||  ||  |  |  ||| | || ||  |||||||||||||||||||||||||| || |||||||| || || |||||||| ||||| |||||||| ||||| |||||||| || |||||||| ||||| |
gtaa--actcagttgttatcaagtgtctcatccataatctaattgtgata-gctttcatgcgtaatgacttctgctttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
gtgattactcgattaattcttcttacagtggtgatagtcatttgaataca-tgtg---ttgctgattgctttcttttcctgttg----tcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
|| ||||    |  || |     ||   |    ||  |||| |        |||    |||  |  || |     ||  ||||     |||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| || |||||||| || ||||| |
gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 9
gtgat-tactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
|| ||  |  |  | ||   ||    ||    |||    |||||  | |   || || |||||  |||||||||    |   ||||||||||| ||||| || || || || || || ||||| || ||||| |||||||| || ||||||||||||||||| || |||||||| || |||||||
gtaatgcatcctgtcaaggtttagcccatacatgactaccattttgaaatgggtatttctgat-actttcttttgtactctacagCGTGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------gtgattactcgatt--aattcttcttacagtggtgatagtcatttgaatacatgtgttgctgatt-gctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
               | ||     | ||  ||||    | |  |  | |  ||  ||     |   ||| | | ||||   ||   ||||||  ||  |||||| |||| ||||| || || || ||||| || || || |||||||| ||||||||||| || || ||||||||||| ||||| |||||||| || || |
atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtat-gttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
---------gtgattactcgatta-attcttcttacagtggtgatagtcatttgaata---catgtgttg-ctgattgct--ttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
          | || |||  | || |||  | |   | |       ||  | ||||||   || || ||  ||  ||| |  || || |||  ||  |||||| | || ||||| || ||||||||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| || ||||| || || || |
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------gtgattactcgattaattcttcttaca----gtggtg-atagtcat--ttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
              || |  ||||||  | ||| | |      |  || |  | ||   || ||| | | || | ||  ||  |   ||  ||  ||  |||||  | || ||||| || || || ||||| ||||| || ||||| |||||||||||||| ||||| |||||||| || || |||||||| |||||||| |
tgtgttgggaatccatgaaccgattatgttttcgtgctttttatattgcactgccaacgttaaattcctttgcttctattt--tgaattgccccttttgcagCGAATACTGGATGCTCTGTTTCCGTCTGTCCTTGGAGGTACCTGCGCCATTCCTGGTGCATTTGGTTGTGGGAAGACCGTCATCAGTCAAGCACTTTCTA

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 8
gtgattactcgattaattcttcttacagtg-gtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                           ||  |||| | |   |||  |  |  |   |||||   ||  | ||||||     |||||  || | ||||| || || ||||| || || || ||||||||||| ||||| || || ||||||||||| || || ||||| |||||||| ||||| |
---------------------------gtatgtgaaattttattg--tcgagctagagctga--actggcctttcctt---acagCGCATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

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|124973576|gb|EL047191.1|EL047191
EST:     GATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|116482299|gb|EG524891.1|EG524891
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|164119617|gb|ES110999.1|ES110999
EST:     TCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: TCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|164221241|gb|ES198925.1|ES198925
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTC
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTC
EST: gi|116482298|gb|EG524890.1|EG524890
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|164008393|gb|ES142261.1|ES142261
EST:     TCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGTCCCTTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCA
genomic: TCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATG-CCC-TTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA
                          tgctgat  putative branch site (score: 3)
                                ttgctttcttttcctg  CT-rich tract
          atttgaata  TA-rich tract