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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA

Basic information

species Arabidopsis thaliana
transcript AT5G23670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctc-gtgtttactgc-ttgatgactaatgtttatctccgttttgcttca-agGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                                     | |||    ||     |   |     ||||  |   | |  | |   | | | || ||||| | ||| |||   | |||    |   |   | | | |||| ||||||| || |   | || ||| | |||||||| ||||||||||||||||| |||||||||||||| |||||||  ||||||||  | ||
-----------------------------------------------------ggatt----ttgcatgactctgttatgttgcaaggttatctccttcaattatttcagtgttaattgcattggatattaaccaatccatatttatggtttcacagGATTGCTTCGGTAGGCCCATAGCAAGTGCACCAGATGCTTGGTTTGATGTTGTTGAGCGCTACTCCAATGACAGTAACAAGACATTAAA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g70360.1 (Oryza sativa), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                          |   |||||   | |  ||   ||||| | |  ||   ||     |||||   |   ||  |  || ||| |  | ||  | ||         ||  | ||| |   |  |||| ||||| |  ||||| ||| | ||    |||||||| ||||| |||||||||||||||||||| | ||||| ||||||||| ||  |
------------------------------------------acgaattatgtacttactaac-atgcatggtg-aattatta-atctgtttaattctcgatctgttcttgtgtttttctgaacga---------attactgttctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttca--agGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                                 | ||  || |||  |   |     |||| |  |  ||||| |    | ||   || ||  |||||  ||  |  | | | |  ||   ||     ||    |   |||| |||||||  || || ||  | || ||||| |||||||||||||| ||||||||||| ||||| |||||||  |||||||| ||  |
-------------------------------------------------actg-tatcgtaagttcactg--cttaaactcta-gaatgatgtattaatc--ttccttttgtttg-tgtgtcgttattgactttgtgctgtcaattatcacggcagGACTGTTTTGGCCGGCCAATTGCTAGCGCACCAGATGCTTGGTTTGACGTGGTTGAGCGTTACTCAAATGACAGTAACAAGACACTGCA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttca---agGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                                       | | ||| |||  |  |||| |   |  |  ||||||   |   ||| ||   || || | ||  | |||  ||     ||| |   | |||   ||   |||| || |||   ||||| ||| | ||    || || || ||||| |||||||||||||||||||| ||||||| ||||||||| ||  |
-----------------------------------------------------ataat-tagctatttagacttttaaattattagatgttttatt---gagatttgtgttttaattggcttatgtttatcaactatatatatgttgtcacatgcagGACTGCTTTTGGCGACCAATAGCCAGCAAGCCGGACGCATGGTTCGATGTGGTTGAGCGCTACTCAAATGACAGCAACAAGACACTCCA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcat-tgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                              ||  |||| || || ||   | ||   ||| | | || |      |     |||   | | | | |||| ||  ||||    |||| |  || ||| |  |      |||| || ||||  || || ||  | |||||||| ||||||||||| |||||||||||||||||||| ||||||  ||||||||| ||  |
---------------------------------------------aatgcttggtatgtgaagggttacag--tttcaccatt-tacccactgatgctatatctatttag-gtttccttgttgacttataatctcaatttccatgat------agGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                               |||   | ||| |  |  |  | |      |  |   |  ||||| ||| |  |   |   |    |   | |  || || |||   |  ||  ||  |  | || |||||| ||||   | || ||| | |||||||||||| | ||||||||||| |||||||||  ||| || ||||| ||||||||  |  |
-----------------------------------------------ttacatgtattttcctggttaatgtc---ggattcaagtctgttttgctaagcaagattgtgcacctcaggat--ataaccaatccgt-cctttgtggttttaca-gGATTGCTTTGGTAGGCCGATAGCAAGTGCACCTGATTCATGGTTTGATGTTGTTGAGCGCACCTCAAACGACAATAACAAGACATTACA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                            ||| || | | || | | | ||  | |   | |||  ||    | | ||  || |||  || |   ||||     || || | |  | ||| | |  |||||    || ||| |||||||   |||| ||  | ||||| |||||||||||||||||||| || || |||||||| ||||| ||||||||||| || ||
------------------------------------------tgtgactactag-atcgca-tcata-atgtaattagcaatgcaggtatgtga-ttgtga-cttatgaagttt-----tttataattttttttt-tgtttgttttttcgca-gGACTGTTTTGGGAGACCAATTGCAAGTGCTCCTGATGCTTGGTTTGATGTTGTCGAACGCTACTCGAATGATAACAACAAGACACTGAA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                      |   | | |  | | ||||| ||   ||| |     | |||  ||   || ||||  || |||  || |   ||||     || || | |  | | | | |  ||||| |    |||| |||||||   |||| ||  ||||||| |||||||| ||||||||||| || || ||| |||| ||||| ||||||||||| || ||
-------------------------------------gtgtgactaacgaatcgcattcta---atgtag----ttagcaatgcagatatttga-ttgtga-cttataaagttt-----ttaataaattttttctgtttg-gtttttcgc--agGACTGTTTTGGGAGACCAATTGCGAGTGCTCCTGATGCATGGTTTGATGTAGTCGAACGCCACTCGAATGATAACAACAAGACACTGAA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgt-tgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                                |||||      || ||||  ||  || | |  | |||| || | |  |   ||| ||   |   |  |     ||||   | || || ||||   ||    |   |||| || |||| | |||| ||||| ||||| |||||||||||||| |||||| | || ||  |||| |||||||| ||||||||  | ||
------------------------------------------------tattgcttggatatttata-aaatttcatgtttatgtgcatttgttcccattgaattatccacataaatg---tgatttttcatattgatct---ttccattgacagGACTGCTTTGGAAGACCAATATCAAGTGCTCCTGATGCTTGGTTAGATGTGATCGAACGTAACTCCAATGACAATAACAAGACATTGAA

upper sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                                                | || |  || |   |    ||    |    ||| ||| || | || |      ||   |   |  | |   | |  | || |   ||| |  | |     || |||| |||||||  || || ||||||||||| || ||||||||||||||||| |||||  | | ||| |||||||| |||||||| || ||
------------------------------------------------ttttcgtgtt-tgactgctaaa----ttgatgttttgattgatcggatgcatgattcagcagctcaaatttgtaactaatattccatatgtt-gatgaatatccagGACTGTTTTGGCCGGCCAATATCGAGTGCTCCAGATGCTTGGTTTGATGTAGTTGAAAGGTTCTCCAATGACAATAACAAGACACTAAA

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|125098987|gb|EL154953.1|EL154953
EST:     GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAG                         GATTGTTTTGAACGACCTATATCGAGCGCACCTGATGCTTGG
genomic: GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAGgtaaattcat ... ttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGG
EST: gi|116422598|gb|EG465190.1|EG465190
EST:     GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAG                         GATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
genomic: GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAGgtaaattcat ... ttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
EST: gi|116471346|gb|EG513938.1|EG513938
EST:     GTTTGGGGCATGAGAATTTCTATATCAGGCGATTGTATCATCGGATTCAG                         GATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
genomic: GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAGgtaaattcat ... ttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
EST: gi|116471526|gb|EG514118.1|EG514118
EST:     GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAG                         GATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
genomic: GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAGgtaaattcat ... ttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
EST: gi|116471371|gb|EG513963.1|EG513963
EST:     GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAG                         GATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG
genomic: GTTTGGGGCATGAGGATTTCTATATCAGGCGATTGTATCATCGGATTCAGgtaaattcat ... ttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA
                         gactaat  putative branch site (score: 2)
                                     tctccgttttgcttc  putative PPT
                            taatgtttat  TA-rich tract