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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggctttatcttcttcgatcttcgccctttagtagatcggatttagcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag

Basic information

species Arabidopsis thaliana
transcript AT2G27020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os05g41180.1 (Oryza sativa), 5'ss of exon 2
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttag--ttggctttatcttcttcgatctt----cgccctttagtagatcggatttagcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag
||||||| || ||||| || ||||| ||||||||||| ||||| || ||||||||||| |||||| | ||||| || |  || || ||||||||||| ||||| |  || | || | | ||  |  | ||      ||||||  | |   |  || | |||      |   |||  || || |  |     |                                             
GTAGCATAGGGACTGGTTATGATCTTTCCGTCACCACCTTCTCCCCAGATGGCCGTGTCTTCCAGGTTGAGTATGCTGGCAAGGCCGTCGACAACAGCGGgttcgatttagtttcaccctcccctctgttttattacccttttttgggctg--ttcaacttt-----atgctgaagttctgatgttttttgcag-------------------------------------------

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 2
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggctttatcttcttcgatcttcgccctttagtagatcggatttagcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag
| ||||| || || || |||||||| ||||| ||||| |||||||| ||||| || || |||||| | ||||| ||| | || |||||||||||||| ||||| | |     |     | |   | | |  ||||| |          ||   |||||     | ||  ||| ||  ||  |||      ||   |||||||| ||                         
GCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGCCACGAAGGCTGTCGACAACAGCGGgttcggtttaactgctcccctttctttccttccttttgctaccgcttcttcctttctg-----tgtgcaattatg--taatgacgtt--ctaatatttgttaacag-------------------------

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 2
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggctttatcttcttcgatcttcgccctttagtagatcggatttagcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag
| ||||| || || || || ||||| || |||||||| ||||||||||||||||| || |||||| ||||||| ||| | || |||||||||||||| ||||||| |  |  |  || |  |    |||    |||  |      || ||     | |    || ||| || ||  | ||  |  |    | |  ||||| || ||                         
GCAGCATAGGCACAGGTTATGATCTGTCTGTCACCACCTTCTCTCCCGATGGCCGCGTCTTCCAGGTCGAGTATGCCACGAAGGCTGTCGACAACAGCGGgttagattccactgcctcccac----ttcctattttgttttgcttgacttgttccccgttttctatga-atcttattgatgaagcca---tggtatttgtgaatag-------------------------

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagt-tggctttatcttcttcgatcttcgccctttag--tagatcggatttagcttctgaaaactttgagatttt-------ggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag
| ||||| ||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || || ||||| ||||| ||||| ||||| ||     ||| | || ||  ||    |   || |   |  | ||||  ||| || |  ||   ||  ||||||       | || |  |      || |  |||| ||    || |    ||     ||  | | ||
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA05G14330.1 (Glycine max), 5'ss of exon 1
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagt---tggctttatcttcttcgatcttcgccct-ttagtaga---tcggatttagcttctgaaaactttga----gattttggttatcgacacgaattagggtttgtta----aaagtctttccctttttttttcttcgcag----------------------------
||||||| || || || |||||||| || |||||||||||||| || |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||| ||   |  | ||||  |  |   | ||     | ||| || |   |   |||     | | |||| |   |    || |||  |||   |     | || | ||| ||     |||   |||     ||||| | || | ||                            
GTAGCATCGGTACAGGTTACGATCTATCGGTCACCACTTTCTCCCCTGATGGCCGCGTTTTCCAGATCGAGTATGCCGCTAAAGCCGTCGACAACAGCGGgttggtacttatcattattattattattattattattattattatacttttaaattcgtggttttaaaattgaaaaaaagagtttatttaataattatgagtatgttttttttttttaaatgattttgtaatttttgtattggtagtgatcttagatttgaaactttgttgcag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 1
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggctttatcttcttcgatcttcgccctttagtagatcggatttagct-tctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag
| ||||| |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||| ||||| |||||| ||  ||  |||||||    | ||     |||  |  | |  | | | || | ||    ||  || |    |||    || | |||    ||    | |||| |                        
GCAGCATAGGAACTGGATACGATCTCTCTGTCACCACATTCTCTCCTGATGGCCGCGTTTTCCAGATCGAATACGCCGCCAAAGCTGTCGATAACAGCGGgttaatt--ctccatcttctctttttttttttttttttttaacctaaatcatctgtttggttgctaagaaa---gggtgggagaaatgaac---ggaacctcaaaatt------------------------

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|47830869|gb|CK120553.1|CK120553
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
EST: gi|124705969|gb|EH797371.1|EH797371
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAA
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAA
EST: gi|86034497|gb|DR330250.1|DR330250
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
EST: gi|86034502|gb|DR330255.1|DR330255
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
EST: gi|86034500|gb|DR330253.1|DR330253
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
EST: gi|47830430|gb|CK120114.1|CK120114
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
EST: gi|86034499|gb|DR330252.1|DR330252
EST:     GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGG                         GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG
genomic: GGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggc ... ttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagttggctttatcttcttcgatcttcgccctttagtagatcggatttagcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG