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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatctttttctgattccaattcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttgagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 6
gtacaaatctttttctgatt-ccaattcatgtatttctgcactttctcagctatttgct--caaatcacattctttggttgagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
|||||  |    || |  ||  |||| |||| |  |   ||  || |     |     |   |||    | | |||   ||    ||||||||||| || || ||||| ||||||||| | || |||||||||||||| ||||| || || ||||||||||| || ||  | || |||
gtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgc---tacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------gtacaaatctttt--tctgattccaattcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttgagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
                                                  | |||||  | |  | | ||   ||      ||||     |  |       ||||      || ||  ||  ||  ||    | ||||||| || || || ||||| ||||| ||||||||||||||||| ||||| || ||||| || ||||| ||||| || || || || |||
gtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatg-acagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAACCAACTCGATGGATTTAGTAGTGACGAGCGGATAAAG

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------------------gtacaaatctttttctgattccaattcatgta------tttctgcactttctcagctatttgctcaaatcacattctttggttgag-------agtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG------------
                                                                                                     | |   |||||| || ||| | ||  ||||      |   |    ||    ||    ||     |  ||   ||  |  ||  |        |||||||||||| ||||| || || ||||| ||| |||| |||||||| ||  | |||||||| || |||||||| ||||||||  | || |||            
gtatgttttgtatgacattttcagttcatgcatgattttattcctgttttggctgatgatactctttataggatgaaaatgttaatcgcctatacaggatcagagcactttttttgtttcaatttagtgtaaacaaatcattcttattaggaagaagcttatctgatgcatgctccataattttgttctcttggtacagTGAAGTTAGCGGTGATAGAGAAGTTCAGCGGACAATGTTGGAATTATTGAATCAACTGGATGGATTCAGCAGCGATGAGAGAATAAAGGTCATAGCTGCA

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
-gtacaaatctttttctgattccaattcat------gtatttctgcactttctcagct---atttgctcaaatcacattctttggttgag---agtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
  ||| |    || ||   | | |||| |       | |    |||  ||| | ||        |   | |||    ||||||| || |    | ||||||||||| || || || || |||||||| ||||| |||||||| ||||| || || ||||| ||||| || ||||||||  | || |||
catacgatgtgttctcctttactaattaacttgtgagcacaattgctttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 6
----------------------------------------gtacaaatctttttctg-attccaa-----ttcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttga-gagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
                                           |   | ||||| || |||   |      |  |   | | |  |   |  ||| | |     |   | |  || || |||||  || | ||||||||| || ||||||||||| || ||| | || ||||| || ||||||||||| ||||| || || ||||| ||||| || ||||||
gtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcagTGAAGTAAGTGGAGACAGGGAGGTACAGCGAACAATGTTAGAATTGCTCAATCAGCTTGATGGTTTTAGTAGTGATGACCGGATTAAG

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------gtacaaatctttttctgattccaatt-catgtatttctgc---actttctcagctat-------ttgctcaaatcacattctttggttgagagta-cagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
                                        |  | | | ||||  ||       | ||  ||| |  |    | |   |    |||       ||  |     |    |||| |||| |   |  ||||||||| || |||||  | ||||||||||| |||||| |||||||||| ||||| || || |||||||| || ||||| || ||||| 
gtttgtaatgttctcttcaaagtgtctatacagaacatcttgtagagcgtttttagaggaagggtacacttatcttggtcaaattgattatattatgacaatcttatttgtgacttgatcttcggtttatgttggcagTGAAGTAAGTGGAGATCGTGAAGTGCAGAGAACTATGCTGGAGTTGCTTAATCAGCTGGATGGATTCAGCAGTGATGAGCGCATTAAA

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|164168558|gb|ES038937.1|ES038937
EST:     ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGAC
genomic: ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGAC
EST: gi|86064649|gb|DR360406.1|DR360406
EST:     ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGG
genomic: ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGG
EST: gi|125051805|gb|EL123881.1|EL123881
EST:     CAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTC
genomic: CAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTC
EST: gi|164022373|gb|ES214096.1|ES214096
EST:     TTATCTTCATAGATGAAATCGATGCCATTAGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGAC
genomic: TTATCTTCATAGATGAAATCGATGCCATT-GGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGAC
EST: gi|164029182|gb|ES157024.1|ES157024
EST:     ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTT
genomic: ATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTT
EST: gi|164030444|gb|ES135268.1|ES135268
EST:     TAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAA
genomic: TAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAA
EST: gi|164030580|gb|ES146709.1|ES146709
EST:     TTATCTTCATTAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAG                         TGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTT
genomic: TTATCTTCA-TAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatct ... gagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgcactttctcagctatttgctcaaatcacattctttggttgagagtacagTGAAGTCAGCGGAGACAGGGAAGTGCAGAGGACTATGTTGGAGTTGCTCAATCAACTTGACGGATTCAGTAGCGATGAACGTATTAAG
                                  attcttt  TA-rich tract