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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAAGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatcaaattttatggctttataaatctcaggtttcgtataaaatttattgtattaatggttgttgtgtctctgttttaatgttgctatcacag

Basic information

species Arabidopsis thaliana
transcript AT1G73230.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g34180.1 (Oryza sativa), 5'ss of exon 3
CAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAAGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatcaaattttatggctttataaatctcaggtttcgtataaaatttattgtattaatggttgttgtgtctctgttttaatgttgctatcacag
||||||||||| || ||||| ||||| ||  |||| || | ||||||||| ||||||||||| ||||||||||| || ||||||||  | || ||||||||| | |      | || |   ||    |||   || |||    |  |   ||| |    || | | | |  | | | |  |||  || |  | |  |||
CAGAGCACTCTGAAAAGAGTAGGAGTAAACACCATCCCTGGCATTGAAGAGGTTAACATTTTCAAGGATGATGTGGTTATTCAGTTTCTGAATCCTAAAGgtgagatc----acttgaatact----aaaatgcaagttctacacga---ttagtaatctacttgctttcttatattttatttcttggttttgttccag

upper sequence: AT1G73230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G131577_T02 (Zea mays), 5'ss of exon 2
CAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAAGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatcaaattttatggctttataaatctcaggtttcgtataaaatttattgt--attaatggttgttgtgtctctgttttaatgttgctatcacag
|||||||| || || ||| | ||||| ||  ||||||| |  |||||||| || ||||| |||||||||||||| || ||||||||  | || ||||||||||| | |      |  |   |    ||     |||| || |||    | ||||| |  |  |||  || || |||  |  ||                  
CAGAGCACCCTGAAAAGAATAGGAGTGAACACCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTGAATCCTAAAGgtaagatac-----tccagaccccagtactcaacaggattagtacttgacttattttctaacaatattttttttgttccccttcag---------------

upper sequence: AT1G73230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G001887_T03 (Zea mays), 5'ss of exon 3
CAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAAGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatcaaattttatggctttataaatctcaggtttcgtataaaatttattg-tattaatggttgttgtgtctctgttttaatgttgctatcacag
|| |||||  | || ||| | ||||| ||   |||||| |  |||||||| || ||||| |||||||||||||| || ||||||||  | || ||||||||||  | |      | |         ||     || | || |||    | |||||  ||  |||  ||  || ||  |  |                   
CAAAGCACCTTGAAAAGAATAGGAGTGAACAGCATTCCTGGTATTGAAGAGGTCAACATCTTTAAGGATGATGTTGTTATTCAGTTTGTAAATCCTAAAGgtatgatac-----tctggactccagtactcaacaagattagtacttcacttatttctaaaaatattttgtgggttcccctccag---------------

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|116447703|gb|EG490295.1|EG490295
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
EST: gi|164180058|gb|ES157850.1|ES157850
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGT
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGT
EST: gi|124779609|gb|EH869552.1|EH869552
EST:     TAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
genomic: TAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
EST: gi|124882565|gb|EH961467.1|EH961467
EST:     TGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
genomic: TGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
EST: gi|125202183|gb|EL217137.1|EL217137
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTACATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGG
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGG
EST: gi|124831745|gb|EH916184.1|EH916184
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACA
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACA
EST: gi|116447701|gb|EG490293.1|EG490293
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
EST: gi|86084370|gb|DR380129.1|DR380129
EST:     AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAG                         TTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA
genomic: AGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatc ... gctatcacagTTCAAGCTTCAATTGCTGCTAACACATGGGTTGTGAGTGGTACACCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAAGTTAACATTTTTAAGGATGATGTAGTCATTCAGTTCATTAACCCTAAAGgtaaaacatcaaattttatggctttataaatctcaggtttcgtataaaatttattgtattaatggttgttgtgtctctgttttaatgttgctatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG