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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTTGTGCTCTCTTTGAACAAGCTATTAAAGAATCAAGAGGGGAGAGCATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttactaaacttggtgacactatgaagcttaaaacgtttttcaaagggtttcttatccagtaattcagaatctactcaccatttgtaaacttgaacag

Basic information

species Arabidopsis thaliana
transcript AT3G02410.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02410.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
CTTCTTGTGCTCTCTTTGAACAAGCTATTAAAGAATCAAGAGGGGAGAGCATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttactaaacttggtgacactatgaagcttaaaacgtttttcaaagggtttcttatccagtaattcagaatctactcaccatttgtaaacttgaacag--------
|  | || ||||| || ||||||||   ||||||||| || || |||   || |||||||||||  |||| || ||||| ||||||||||| ||||||||||    ||     |||  | |    ||   | || |    | | ||     | || | |||   | ||| |  |  | ||   | |  ||   |||||  ||        
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggata----gctttatcatctaattttgattgat-tatatgtctgtatggttatcatc--attattaaagaattgcttctcctgagt---cttgattagttttctat

upper sequence: AT3G02410.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv14s0006g00430.t01 (Vitis vinifera), 5'ss of exon 7
CTTCTTGTGCTCTCTTTGAACAAGCTATTAAAGAATCAAG---AGGGGAGAGCATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttactaaacttggtgacactatgaagctt--aaaacgtttttca--aagggtttcttatccagtaa--ttcagaatctactcaccatttgtaaacttgaacag
   ||||||||||| |  | || || || || || || ||   ||| || | ||| || |||||||| |||||||| |||||||| ||||||||||||||||||||| |   ||  |    || |  ||| ||  ||   |||   | ||||  |||  ||| |  |  |  ||  ||||| | |||  |  ||||| ||||         
---CTTGTGCTCTCCTAAATCAGGCAATCAAGGAGTCTAGGGAAGGAGATATCATGTCTTGGAGTGTTTCTCAGATAAAAGCTTATTTTGGTTTATCTGGAGGgtaaatatttattcactatgtcgttataaatttttggaaatcctcttcatgaagcctttatgttttaaaaaacttcaggacctaggcttcatttttaaat--------
















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|116389289|gb|EG431881.1|EG431881
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCGAGGCTTGTATCG
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCGAGGCTTGTATCG
EST: gi|116389287|gb|EG431879.1|EG431879
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTTATCTGGTTGAACACTTCCACAACCGAGGCTTGTATCG
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCGAGGCTTGTATCG
EST: gi|116389292|gb|EG431884.1|EG431884
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCGA
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCGA
EST: gi|116389288|gb|EG431880.1|EG431880
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         AAACAATCTCTTTAATCTGGTTGAACACTTCCACAAC
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAAC
EST: gi|116389291|gb|EG431883.1|EG431883
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTAATCTGGTTGAACACTTCCA
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCA
EST: gi|116389290|gb|EG431882.1|EG431882
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GAACAATCTCTTTAATCTGGTTGAACACTTCCACAACC
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACC
EST: gi|116389281|gb|EG431873.1|EG431873
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCG
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACCG
EST: gi|116389279|gb|EG431871.1|EG431871
EST:     ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGG                         GTACAATCTCTTTAATCTGGTTGAACACTTCCACAACC
genomic: ATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttact ... acttgaacagGTACAATCTCTTTAATCTGGTTGAACACTTCCACAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTTGTGCTCTCTTTGAACAAGCTATTAAAGAATCAAGAGGGGAGAGCATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttactaaacttggtgacactatgaagcttaaaacgtttttcaaagggtttcttatccagtaattcagaatctactcaccatttgtaaacttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG