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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag

Basic information

species Arabidopsis thaliana
transcript AT3G18780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g64630.1 (Oryza sativa), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacatttt------aggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag-------------------------------
||||||||||| || |||||||| |||||||| ||||  || || ||||| || |||||||| || ||||| || ||||||||||||||||| ||||| |||  |   |||        |         |||    | |   ||  |||| | ||   |  |    |||   |||| |||  ||                               
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACTGCCCAGCGATGTACGTTGCCATCCAGGCCGTTCTTTCGTTGTACGCCAGTGGTCGAACAACTGgtatgatgattgctgtacaaaaaaaaccatttgattttaac-atacttatctaaaaaaaattgattttaatatccaatgagtagtcgaactgcgctaactagtttataaatgcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag---
||||||||||| || ||||||||||||||||| || |  || || ||||||||||| ||||| |||||||| |||||||| || || ||||| ||||| |||  |   ||| |   ||||    |    |   || |  |||   ||   || |      | |   | | || | | |   
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatg---attattacctttgcaatagatcgtgttaaa-attcaatgtgttggggggcagtgacacttcttttatctgcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag
||||||||||| || |||||||||||||| || ||    || |||||||||||||||||||| || || |||||| |||| |||||||| |||||||| ||| |  ||   | |  |   | ||| | | |  || |  | ||||     |   |    | | |    | |    |||
GAGAAGATGACCCAGATCATGTTTGAGACTTTCAATGTGCCAGCTATGTATGTCGCCATCCAGGCCGTGCTCTCCCTGTATGCCAGTGGACGTACAACTGgtaataac---tcactcacatggttgagagtt-ttaaaaaatattcactttattcatgaactgttgctcttgatgcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g64630.2 (Oryza sativa), 5'ss of exon 3
-------------------------------------GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag
                                     ||||||||||| || |||||||| |||||||| ||||  || || ||||| || |||||||| || ||||| || ||||||||||||||||| ||||| |||  |        | | ||  |||  | |       |  |  ||||||  | | |  |  ||||||   |   |    
GCTGACCGAGGCTCCTATGAACCCCAAGGCAAACAGAGAGAAGATGACCCAGATCATGTTCGAGACCTTCAACTGCCCAGCGATGTACGTTGCCATCCAGgccgttctttcgttgtacgccagtggtcgaacaactggtatg--------atgattgctgtacaaa------aaaaaccatttgattttaaca-tacttatctaaaaaaaattga

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g61970.1 (Oryza sativa), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGg--ttagtacattttaggctttttg-----------tttatactcattgatcattatt--tgaactgagctctgattatcttccattgaacag
||||| ||||| ||||||||||||||||| || ||  | || || |||||||| || || ||||||||||| ||  | || ||||||||||||||||| ||  |  || ||||||   || ||             | || ||| |    || | |||  |||  ||| | | |    |  |   |||  |||
GAGAAAATGACCCAAATCATGTTTGAGACATTCAATGCACCAGCAATGTATGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAGgcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G126190_T02 (Zea mays), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcatt--gatc------attatttgaactgagctctg-attatcttccattgaacag
||||||||||| |||||||||||||||||||| ||   ||| || ||||||||||||||||| ||||| || ||| ||||||||||||| |||||||| ||| |  |   ||||   |  |     |   |||||  ||        ||| ||  | || |  | || |||    | | || |    
GAGAAGATGACCCAAATCATGTTTGAGACCTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGGCGTACAACTGgtaatgattctttaacatggtgaccaaatttcattaggacttcccaaatttttccatctcaattatggattgctgttccttcag---

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G006765_T02 (Zea mays), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcatt--gatc-----attatttgaactgagctctga-ttatcttccattgaacag
||||||||||| ||||||||||||||||| || ||   ||| || ||||||||||||||||| ||||| || ||| ||||||||||||| |||||||| ||| |  ||   ||    |        |   |||||  ||       ||| |   | || |  | ||  ||    | |||    |||
GAGAAGATGACCCAAATCATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G437445_T01 (Zea mays), 5'ss of exon 4
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgt-tagtac-attttaggctttttgtttatactcatt-gatcattatttgaactgagctctgattatcttccattgaacag
||||||||||| || || ||||| ||||| || ||||  || || |||||||| |||||||| || ||||| ||| |||||||||||||||| ||||| ||| |  |||    |||    | ||   |||   ||||  |  | || | | | | ||   |    ||||| |         
GAGAAGATGACCCAGATTATGTTCGAGACATTCAACTGCCCAGCAATGTATGTGGCCATCCAGGCCGTTCTTTCCCTGTACGCCAGTGGTCGAACAACGGgtatgttactgcattaaatctgtttcatatcagcattcaaataatagt-gtagtcagtgataggaatctttctgcag----

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G053284_T01 (Zea mays), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgt-tagtacattttag----------gctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag
||||||||||| || |||||||||||||| || | ||  || || ||||||||  ||||||| || ||||| ||| ||||||||||||| || || || |||    ||| ||   |          | ||  |||    | ||    | || ||  || | ||||    ||  ||||| |  ||  |||
GAGAAGATGACCCAGATCATGTTTGAGACGTTCAGCTGCCCGGCAATGTATGTGTCCATCCAGGCCGTTCTTTCCCTGTACGCCAGTGGACGAACGACTGgtacgttacgttgctgcatcgaacctgtttcatgtcagcattcgaatagcagtacgtgtagtgagtggcgacaatctttc--tgtgcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 2
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccatt--gaacag
|| |||||||| |||||||||||||||||||| ||    || || |||||||| |||||||| ||||||||||||||||| ||||||||||| ||||| |||| ||| |||     || | |   |  | || || || || |  | |      | |||| |   |||| ||   |||||
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCCAGTGGTCGCACAACTGgtttgtatattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatcaattcctttcaaaacag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccatt--gaacag
|| |||||||| |||||||||||||||||||| ||    || || |||||||| |||||||| ||||||||||||||||| || |||||||| ||||| |||| ||| ||      || | |   |  | || || || || |  |        | |||| |   |||| ||   |||||
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCAAGTGGTCGCACAACTGgtttgtatatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatcaattccttttaaaacag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G39380.2 (Glycine max), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcat----tgatcattatttgaactgagctctgatt---atcttccattgaacag
|| || ||||| |||||||||||||||||||| ||    || || |||||||| |||||||||||||| |||||| | || || |||||||| ||||| |||| |||  |||    |  | |||||  | ||||    |  |||| |  |        | |||| |   ||  |   |  |||||
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAAGCTGTCCTCTCCCTATATGCAAGTGGTCGCACAACTGgtttgta--tttgtatccatctgtttcaattcatagttttgtcatcacattgttctttccctgaatcaaatactttctgaaacag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 3
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtac--attttaggctttttgtttatactcattgatcattat-ttgaactgagctctgattatcttccattgaa-cag
|| || ||||| |||||||||||||||||||| ||    || || |||||||| |||||||| ||||| |||||| | || || |||||||| ||||| |||| ||||  ||||    || | |   |  |||| ||  || | |  |||  ||   ||   || |  |    ||||| |||
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTCCTCTCCCTATATGCAAGTGGTCGCACAACTGgtttgtacttatttccatctgtcttaattcactcctttgtcttcacattgttctatccttgaatcaaatctttttgaatcag

upper sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 4
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagta-------cattttaggct-----ttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag
|| |||||||||||||||||||||||||| |||||    || || |||||||| ||||| || |||||||| ||  | || |||||||| |||||||| |||| |||       | |||| |  |     |||  ||| |  |   || |  |  | |   ||||| ||| | | |  ||| ||||  ||
GAAAAGATGACTCAAATCATGTTTGAGACTTTTAATGTGCCTGCCATGTATGTTGCCATTCAGGCTGTTCTTTCTCTATATGCCAGTGGGCGTACAACTGgttcgtattaaaatctttttggattggaattttcatttttcttttctgttgttagtgtagcctgagttctaact-tgctcctttgactag

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|125015870|gb|EL088139.1|EL088139
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGACTGGATTCT
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTG-CTGGATTCT
EST: gi|125198932|gb|EL213886.1|EL213886
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTG
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTG
EST: gi|116435189|gb|EG477781.1|EG477781
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
EST: gi|125163913|gb|EL190683.1|EL190683
EST:     CTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
genomic: CTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
EST: gi|125205562|gb|EL220516.1|EL220516
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACT
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACT
EST: gi|124809133|gb|EH894893.1|EH894893
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGG
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGG
EST: gi|125297214|gb|EL311299.1|EL311299
EST:     GTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATT
genomic: GTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATT
EST: gi|125206322|gb|EL221276.1|EL221276
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTG
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTG
EST: gi|124968367|gb|EL042328.1|EL042328
EST:     CTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
genomic: CTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
EST: gi|124910842|gb|EH984922.1|EH984922
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGT
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGT
EST: gi|124824956|gb|EH909822.1|EH909822
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCT
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCT
EST: gi|116486734|gb|EG529326.1|EG529326
EST:     TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCG                         GTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
genomic: TGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG
EST: gi|152034980|gb|BP841345.2|BP841345
EST:     TGGTCGTACAACCG                         GTATAGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTGCG
genomic: TGGTCGTACAACCGgttagtacat ... cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT