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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC

Basic information

species Arabidopsis thaliana
transcript AT3G51850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 6
agagagttcacttctcatatcgttaaacagaaccttagagactatagt-tagtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
           |  | ||||   | || | |||| |        || | | ||  |||| | ||| || |     |  |  |  |    |||| ||   ||||||| |  || ||||| || || ||||  ||||||||||| || || || ||||||||||||||||| || |||||||| ||||| |||||||| ||||
----------gtgatgatatttctgaatacaaccattcttttggtaatatcgttcaaaacttttttttatctaaataacatatgttttcttttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACAGATTGGAGAAAGGCGTCCCGGCATTACTCTAGAGGAAGATTCAACAGCC

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 6
agagagttcacttctcatatcgttaaacagaaccttagagactatagt-tagtgtaaaaatgtttcttctggttgtgcctgacatg--gatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
                 |   | |  ||  ||   | |   | ||  | ||   |  | || ||    ||     |  |  ||||   |||  || |  | ||||||| | ||| ||||| ||||| || |  ||||||||||| || || || ||||||||||||||||| || ||||| ||||||||  | ||||| ||||
----------------gtgatgattcact-aatgctggtagcaatgatataacctccagatcttatgcctttacttaacaaacatttcgatcgtttat-tcagGATGGCAAAATTAGCTATGAAGAATTCGTAGCAATGATGAAGACTGGCACAGATTGGAGAAAGGCGTCACGGCATTATTCAAGAGGACGTTTCAACAGCC

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 6
--agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
    |  ||||||  || |   |  | |  | | |  |   | ||  |  |    | ||    ||  |||  || |       | | | | |||  |   ||||||| | ||| ||||||||||| ||||  || |||||||| || ||||| |||||||| |||||||| || ||||| ||||||||| | ||||||||||
gttaacggttcac--ctaaggcccctgag-atagctctgctgccttcaaatctcattaa----ttatttcaagtcgcaataacctttgttgttt--ctgcagGATGGTAAAATTAGCTACGAAGAATTTGTAGCGATGATGAAGACTGGAACAGATTGGAGGAAGGCGTCGCGGCATTATTCAAGAGGGCGCTTCAATAGCC

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G311220_T01 (Zea mays), 3'ss of exon 6
agagagttcacttctcatatcgttaa----acagaaccttagagactatagttagt---gtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
 |  | |     |||||| ||  ||     || |    ||   | |    | | ||    | ||   || || || |  | |        |  ||   ||     |||| || |  || |||||||| ||||||| ||| |||||||| || || ||||| |||||||||||||| || || ||||| |||||||| ||||| ||||
-gtcactgacactctcatgtctctagtaggacgggttattttggtcctctggtcgtctgatgaacgagtgtcgtccgtctcttgtccgtttacatcgatgtg--cagGACGGCAAGATCAGCTACGAGGAGTTTGTGGCGATGATGAAGACCGGCACGGACTGGAGAAAGGCGTCCCGGCACTACTCGAGAGGGAGGTTCAACAGCC

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 6
agagagttcacttctcatatcgttaaacagaacc-ttagagactatagtta-gtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacatt-----agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
     ||| ||    ||   |    ||     |    | ||  | | | |  |  |  ||||  |     | ||   |||  | ||   ||   |   ||     ||||||||| ||| |||||||| || ||||  || ||||||||||| || ||||| ||||| ||||| || || || || ||||||||| | ||||||||||
-----gttaacgatccac--caccgaaggctcctgcgatagcttgtggctgtgccttcaaatcctatcgttagtcaggccgca-ataacttcccgttgtttctgcagGATGGGAAAATTAGCTACGACGAATTTGTAGCGATGATGAAAACTGGCACGGACTGGAGGAAGGCATCGCGGCACTATTCAAGAGGGCGCTTCAATAGCC

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctgg-ttgtgcctgacatggatttttgacatt---agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
                            |  |    ||||| | |  ||    || |    |   |   || |  | ||    |    | ||  ||| |   |||||||  | || |||||||| || ||||  || ||||||||||| ||||| ||||||||||| || ||  | ||||||||| | || |||||||||||| 
-----------------------gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttaccctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 8
agagagttcacttctcatatcgttaaacaga-accttagagactatagttagtgtaaaaatgtttcttctgg-ttgtgcctgacatggatttttgacatt---agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC-
                             || |  | ||||| |    ||    || |    |   |   || |  | ||  | |    | ||  ||| |   |||||||  | || ||||| || || ||||  || ||||||||||| ||||||||||||||||| || ||  | ||||||||  | || |||||||| |||  
---------------------------tggatatttgagagatttctctttacatataggcttgattaggggatcttaccatataaaattcttgaacacttgcaggATGGACGTATCAGCTATGATGAATTTGTTGCTATGATGAAAACTGGAACGGATTGGAGAAAAGCATCAAGGCATTACTCGCGTGGAAGATTCAACAGCTT

upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctggttgtgcctgacatggatttt---tgacatt--agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
                            |  | |    ||  |    | |     |   |  | |  | | || |   |||| |   ||||   | ||| |  ||||||||| ||| || || || || |||||||| ||||||||||| ||||| |||||||||||||| ||| | ||||| ||||||||||||||||| || |
-------------------------gtaaagatccagtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC

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|116407590|gb|EG450182.1|EG450182
EST:     ACTGTGTGGATGTCGCCAATGATATATTCCAAGAAGTTGACACAGACAAG                         GATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACG
genomic: ACTGTGTGGATGTCGCCAATGATATATTCCAAGAAGTTGACACAGACAAGgtaagtgtca ... ttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttagtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC
                                           ttttgac  putative branch site (score: 3)
                                          ttttt  CT-rich tract
        taaaaatgtttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctggttgtgcctgacatggatttttgacattagGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - cttctca
- - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaaa