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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgattccaattcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttgagagtacag

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgt---acaaa---------tctttttctgattccaattcatgtatttctgcactttctcagcta-tttgctcaaatcacattctttggttgagagtacag
|||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| ||||| |  ||||  || || ||||   |||||         || ||      |||| | |  || || | || ||     ||     | |  ||   | |  |  ||      |  ||    
CAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTGGAAGCAAGCACTTTGATAGgtatgacaaacatggtcgttccttcatcatttcccacttttgaatatgtgaacaaatacactaggtcttttctgttaatttctttccagcaattgtttgt

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgatt-ccaattcatgtatttctgcactttctcagctat--ttgctcaaatcacattctttggttgagagtacag
||||||||||||||||||||||||| ||||| || |||||| | || ||||| || || || |||||||| || || ||||| ||||||||||| || |||||||  |    || |  ||  |||| |||| |  |   ||  || |     |   |     |||    | | |||   ||    |||||
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgc---tacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttc-tgattccaattc-----atgtatttctgcactttctcag-ctatttgctcaaatca---cattctt-tggttgagagtacag---------------------------------------
||||||| || || ||||| ||||| ||||| || ||||||||||| ||||| || ||||| ||||| || ||||||||||| || ||| | || ||||||||   || | |  | |||||   || |     |  | || || || | | |||   | | |  |  |||||   ||||||| | |   | | || |                                        
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctt------tttctgattccaattcatgtatttct--gcactttctcagctatttgctcaaatcacattctttggttgagagtacag-----
| ||||||||  | ||||| ||||| ||||| || |||||||| |||||||| ||||| || |||||||| ||||||||||| ||||||||||| ||||||||||  | ||      ||| | || |    | |||| ||||    ||| || | | |||  |       | ||    |||| | || | |  |      
CTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttttatttagtttgtcatccagtctaatgtctttcctaacaccttttaacctacatcagtttgtgaccaagtttgatagacattttaacaagc

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgattccaattcatgtatttctgcactttctcagctatttgctcaaatcacattcttt---ggttgagagtacag-------------------------------------------------------------------------------------------------------------------
||||||||||||| ||||| || || |||||||||||||||||||| || ||||| || || ||||| || ||||||||||| || || ||||| || |||||    |  | |     || || |||||| ||   |  | |       || |||   |  || | | |||||   || ||| | |                                                                                                                       
CAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTGGCACCAAACGTTTTGATAGgtatgttttgtatgacattttcagttcatgcatgattttattc------ctgttttggctgatgatactctttataggatgaaaatgttaatcgcctatacaggatcagagcactttttttgtttcaatttagtgtaaacaaatcattcttattaggaagaagcttatctgatgcatgctccataattttgttctcttggtacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G173849_T01 (Zea mays), 5'ss of exon 2
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgattccaattcatgtatttctgcactttctcagctatttgctcaaatcacattctttg-gttgagagtacag----------------
||||||||||||| ||||| || || |||||||||||||||||||| || ||||| || || ||||| || |||||||| || || || ||||| || |||||    | || |     ||  |  || || ||   |   || |  | ||| || ||| |    ||  | | || | ||| | |                    
CAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCGGCACCAAACGTTTTGATAGgtatgccttttatgacatttttagctcttgcatggtt---ctattcctgct-ttggctgatgatactctttatgagatgaaaatgtgaatcagttgcacaagac

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatc-----tttttctgat-------tccaattcatgtatttctgcactttctcagctattt-gctcaaatcacattctttggttgaga-gtacag-----------------------------------
|||| ||||| ||||||||||||||||| || ||||||||  | || |||||||| || ||||||||||| ||||| ||||||||||||||||| || |||||  |        |  ||  |||       | ||||| |  | |||||    ||| | || ||    | ||| |     ||  || ||| |   ||   |                                   
CAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTGGTACAAAGCGTTTTGATAGgtattagctggcagtaatttagatatacatttgcaattgacttttttctttcttttttgaggtagagagatcaga--gtgttacttagttaaattgtctcggttctaactttgatgtatcttgtggctaattgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G42110.1 (Glycine max), 5'ss of exon 4
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgta----caaatctttttctgattcca---attcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttgagagta-cag---------------------------------------
|||| |||||||| ||||||||||| || || ||||||||  |||| |||||||| || || |||||||| ||||| ||||| |||||||||||||| |||||    |||       | |   || |   |||||| ||| | | |  ||  |    |||| |   |   |   |||||   |  | | || |||                                       
CAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtatgagcaagcaggaatttagatctacgtattcat-tatcttttcttttctttttttattgggaaagggctggttcttgtttcaataatatcagttttgcaaccttgtgatgttatttggttgctggttgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtac-----aaatcttt--ttctgatt--ccaattcatgtatttctgcactttctcagctatttgctcaaatcacattctttggttgagagta-cag---------------------------------------
|||| |||||||  ||||||||||| || || ||||||||  |||| |||||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||       |||||     ||  |||   || |||||| |||  || |  ||| |  | |||| |   |   |   |||||   |  | | || |||                                       
CAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtgtgaggaaaatcaggaatttagatctacctattcat-tatcccttctttttttttg-tattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgattcca-attcatgtatttctgcactttctcagctattt--------gctcaaatcacattctttggttgagagtacag----------------------
|||| ||||| ||||| ||||||||||| || ||||| ||  | || |||||||| || ||||||||||| ||||| ||||| || |||||||| || |||||  |           |||  | || ||| |     ||   ||| |   |    |         ||||  | | ||    |||||   |                            
CAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgattc-caattcatgtatttctgcactttctcagctatttgctcaaatc-acattctttggttgagagtacag-----------------------------------------
| || |||||||||||||||||||| ||||| ||||||||| |||| ||||| || || ||||||||||| |||||||| || |||||||| || || ||||  ||| | || |  | ||  || | ||| | |      | |||       ||    |   ||  | ||| |   | |||    |                                            
CGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAGGCACAAAGCGGTTTGATAGgt--aaaccattattggtttagcactacatctttcatgatatttttatcaaaatggatttggattgaaattatcaaggtgaactcatgagcagcctccttgactatagacttttctgccttttattgcag

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