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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaacaagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G14400.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 2
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaacaagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagaccttt-ttgtttctaaatttgtag
| ||||||||||||||  |  ||  ||| || || || || || || ||||| || |||||||||||||| || ||||| ||||||||||| || ||||||||| | |    |    ||| ||| |   | |  ||   | |     || | |   | |  ||  |||||||   |   || | |||   |||| ||
TGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAACAATATAATGCTTTGGAATGCTGTAATTTTTGGgtaaggtgttaga----cttaagagatatgttttattcctttcggttttattttgatccatta--tacttagttgtcaattatgtcttgttttgcag

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgta--atgggaacaagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag
| ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||| |||||||| ||||| |||||||||||||||||||||||  |||   |      ||      |  |  | |  | ||  |   | || |   ||||     | |  || ||  |  || |||||   |||  ||
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttct---tttacag

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 5'ss of exon 1
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaacaagtacctttagatactggct--aaatatttctgaaacttt---tgtcatttctgtacttacttagacctttttgtttctaaatttgtag------------------------
| |||||||||||||||||| | |||||||| |||||||| || || ||||| ||||| |||||||||||||| ||||| |||||||||||||| |||||||| |     |     |  ||   | ||   |   | |  || |    |||    | |  ||| |  ||||  || ||   || |  ||||   ||| | |                        
TGATGAGGGATTTCAAGAGGCTCCAGCAAGATCCACCTGCTGGCATCAGTGGGGCTCCTCAGGACAACAACATCATGCTATGGAATGCTGTCATTTTTGGgtatttctttctttctctctttctttctttttttgattggttttttgccttaccattttgtttatcaacttgttttgataattctaattctgggtttttggtgttttttcttgtttgatttgtag

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaacaagtacc--tttagatactg---gctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag
| ||| | || |||||| |  ||||||| || || || || || || || || || || |||||||||||||| ||| | ||||||||||||||||| |||||     |       ||  |||   | |||   ||| |||  |   |  |    ||  |  |  ||     |   ||  |||   |  |    |  ||  
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggg-gcgcggagatttgcatggcggtgtcggttt

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaa---caagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag-
| ||| | || |||||| | ||||| || || || || || || || || || ||||| ||||||||||| || ||||| ||||||||||| ||||| |||||| |           |   ||    |  ||   || | | || |    |  ||     |  |       |  ||       ||       |  ||   
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt

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|86077068|gb|DR372825.1|DR372825
EST:     GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGG                         GCCTGATGACACACCATGGGATGGAG
genomic: GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaa ... aaatttgtagGCCTGATGACACACCATGGGATGGAG
EST: gi|301501590|gb|HO207130.1|HO207130
EST:     GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGG                         GCCTGATGACACACCATGGGATGGAG
genomic: GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaa ... aaatttgtagGCCTGATGACACACCATGGGATGGAG
EST: gi|47831557|gb|CK121241.1|CK121241
EST:     GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGG                         GCCTGATGACACACCATGGGATGGAG
genomic: GGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaa ... aaatttgtagGCCTGATGACACACCATGGGATGGAG
EST: gi|124795387|gb|EH885066.1|EH885066
EST:     CTGGAATGCTGTCATATTTGG                         GCCTGATGACACACCATGGGATGGAG
genomic: CTGGAATGCTGTCATATTTGGgtaatgggaa ... aaatttgtagGCCTGATGACACACCATGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgtaatgggaacaagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG