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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaaccattttttatctatacatcagaacctttttttcatgttactgatcattgttcctcctttgaatgttactacag

Basic information

species Arabidopsis thaliana
transcript AT1G17880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17880.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 5'ss of exon 3
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaaccattttttatctatacatcagaacctttttttcatgttactgatcattgttcctcctttgaatgttactacag
|| |||||||| || ||| | ||||| ||| |||| || |  |||||||| |||||||| || ||||||||||| |||||||||||  | || ||||| ||| ||     || ||   |    |     | |  ||  |    |  |  |  |   |  | ||  ||  |   |||  | ||  | |||
CAGAGCACTCTGAAAAGAGTAGGAGTAAACACCATCCCTGGCATTGAAGAGGTTAACATTTTCAAGGATGATGTGGTTATTCAGTTTCTGAATCCTAAAGgtgagatcacttgaatactaaaatgcaagttctacacgattagtaatctacttgctttcttatattttatttcttggtt-ttgttccag

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G131577_T02 (Zea mays), 5'ss of exon 2
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaaccattttttatctatacatcagaacct---ttttttcatgttactgatcattgttcctcctttgaatgttactacag
|| ||||| || || ||||| ||||| ||| ||||||| | ||||||||| || ||||||||||||||||||||||||||||||||  | || ||||| ||||||  | |    |||    |          || || || |   || |||  |   | |  |  || |    || || |            
CAGAGCACCCTGAAAAGAATAGGAGTGAACACCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTGAATCCTAAAGgtaagatactccagaccccagtactcaacaggattagtacttgacttattttctaacaatattttttttgttccccttcag-----------

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G001887_T03 (Zea mays), 5'ss of exon 3
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaaccattttttatctatacatcagaacctttttttcatgttactgatcattgttcctcctttgaatgttactacag
||||||||  | || ||||| ||||| |||  |||||| | ||||||||| || ||||||||||||||||||||||||||||||||  | || ||||| |||| |  | | |  ||      |    ||  || ||  |    |  ||||  ||| |  | |   |   |  | ||  |    || |||
CAAAGCACCTTGAAAAGAATAGGAGTGAACAGCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTAAATCCTAAAGgtatgatactctggac------tccagtactcaacaagattagtacttcac-ttatttctaaaaatattt--tgtgggttcccctccag

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G041881_T02 (Zea mays), 5'ss of exon 3
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt---tttaaccattttttatctatacatcagaacctttttttcatgttactgatcattgttcctcctttgaatgttactacag
|| |||||  | || ||||||||||| ||| | ||||| | |||||| || || |||||||| ||||||||| ||||||| || |||   |||||||| ||||| ||      |   | ||  ||   |||  | || | |    || | | |  |||   ||| || |   |    || |           
CAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAGGTCAACATCTTCAAGGATGATATTGTTATCCAATTCCAGAACCCTAAAGgtaaatcccgccatgcgaacacgttacttctgcatattatagaagttgtctgacattatcaatctttctctgtttcctgcag----------

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 5'ss of exon 3
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaacc--attttttatctatac-atcagaacctttttttcatg-ttactgatcattgttcctcc--tttgaatgttactacag---
|||||||| || |||||||| ||||| ||  |||| || |||||||| || || ||||||||||| |||||||| |||||||||||  | ||||| || ||||| || ||   | |    | |||| | | ||  || |  ||||| |     ||  | |  |  |  | |  | |  ||| ||| ||| ||      
CAAAGCACCCTAAAGAGAATAGGAGTCAATGCCATACCTGCTATTGAGGAGGTCAACATCTTTAAAGATGATGTGGTTATTCAGTTTTTAAACCCCAAAGgtaa-tctttcccagctttgtattttgtttgtatgattattaccttatggcagtgactgccaactaaagctttttcctttttaattttaatatttcag

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|124943428|gb|EL019609.1|EL019609
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTG
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTG
EST: gi|164169455|gb|ES040049.1|ES040049
EST:     AAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: AAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|164103089|gb|ES073802.1|ES073802
EST:     ATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTACTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: ATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|152035741|gb|BP855298.2|BP855298
EST:     AGTTAACATCTTTAAGGATGATGTGGTTATTCAGTTAATCAACCCTAAGG                         TTCAAGCTTCAATGGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|164159100|gb|ES125851.1|ES125851
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCT
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCT
EST: gi|164172589|gb|ES197740.1|ES197740
EST:     TCTTTAAGGATGATGTTGTTATTCAGTTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: TCTTTAAGGATGATGTTGTTATTCAG-TTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|47829080|gb|CK118764.1|CK118764
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|164106414|gb|ES018920.1|ES018920
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATT
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATT
EST: gi|124941995|gb|EL018300.1|EL018300
EST:     ATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: ATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|164129285|gb|ES198032.1|ES198032
EST:     CTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: CTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|124887168|gb|EH966070.1|EH966070
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTG
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTG
EST: gi|124897526|gb|EH973740.1|EH973740
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAAACACATGGGTTGTTAGCGGTTCTCCTCAG
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAA-CACATGGGTTGTTAGCGGTTCTCCTCAG
EST: gi|86074372|gb|DR370129.1|DR370129
EST:     AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: AGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|164162239|gb|ES002841.1|ES002841
EST:     AGTTCATCAACCCTAAGG                         TTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
genomic: AGTTCATCAACCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAATTGCTGCAAACACATGGGTTGTTAGCGGTTCTCCTCAGA
EST: gi|125030438|gb|EL102707.1|EL102707
EST:     GTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAAACCCTAAGG                         TTCAAGCTTCAA
genomic: GTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAA-CCCTAAGGgtaagtcatt ... gttactacagTTCAAGCTTCAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAAGTTAACATCTTTAAGGATGATGTTGTTATTCAGTTCATCAACCCTAAGGgtaagtcatttttaaccattttttatctatacatcagaacctttttttcatgttactgatcattgttcctcctttgaatgttactacag

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