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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcag

Basic information

species Arabidopsis thaliana
transcript AT1G78900.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 9
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtg-----attactcgattaattcttctt-----acagtggtgatagtcatttgaatacatgtg-ttgctgattgctttcttttcctgttgtcag---------------------------------------------------
|  |||||||| ||| | || ||||| |||||||| ||||||||||| ||||| ||||| || || ||||||||      || | | |  |    |||  |     | | |  | |  ||  | | || || ||   ||||  |    ||||   |  |||| |||                                                    
ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtt-tcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcag

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 9
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtc--atttgaatacatgtgttgctgattgctttct-tttcctgttgtcag
|  |||||||||||||| || ||||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |  ||||  ||  | |    |         ||  ||  |||   |||    |  |||| | ||  |||| |||  |   |    
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaa--actcagttgttaccaagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttttttacag----

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 9
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtc--atttgaatacatgtgttgc-tgattgctttcttttcctgttgtcag
|  ||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |  ||||  ||  |      |         ||| ||  |||   |||  | |  ||| | ||  |||    ||  |   |    
ACTTGGCCCGTACGTACACCAAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaa--actcagttgttatcaagtgtctcatccataatctaattgtgatagctttcatgcgtaatgacttctgctttttacag----

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 9
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtcatttgaataca-tgtg---ttgctgattgctttcttttcctgttgtcag-----
|  |||||||||||||| |||||||| ||||| |||||||| ||||| ||||| || |||||||| || ||||| ||||    |  || |     ||   |    ||  |||| |        |||    |||  |  || |     ||  |||| |||      
ACTTGGCCTGTACGTACACCTAGGCCTGTTGCGTCAAAGCTGGCTGCTGATACCCCACTACTTACAGGACAGgtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcctgatttttgtt-tcatctcag

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 9
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgat-tactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcag
|  |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||  |  |  | ||   ||    ||    |||    |||||  | |   || || |||||  |||||||||    |   |||
ACTTGGCCTGTCCGTACACCTAGGCCTGTTGCCTCAAAGCTTGCTGCTGATACACCTCTCCTTACTGGGCAGgtaatgcatcctgtcaaggtttagcccatacatgactaccattttgaaatgggtatttctgat-actttcttttgtactctacag

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|116482298|gb|EG524890.1|EG524890
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|124973576|gb|EL047191.1|EL047191
EST:     GATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|116482299|gb|EG524891.1|EG524891
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|164119617|gb|ES110999.1|ES110999
EST:     TCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
genomic: TCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATT
EST: gi|164221241|gb|ES198925.1|ES198925
EST:     GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGCCCTTTTCCCTTC
genomic: GGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTC
EST: gi|164008393|gb|ES142261.1|ES142261
EST:     TCCTCTACTTACGGGGCAG                         CGTGTTCTTGATGTCCCTTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCA
genomic: TCCTCTACTTACGGGGCAGgtgattactc ... ctgttgtcagCGTGTTCTTGATG-CCC-TTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcctgttgtcag

- - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC