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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG

Basic information

species Arabidopsis thaliana
transcript AT5G55230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 6
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
          ||     |||     |  | | || |||       ||     || |  ||  |   |    | |     |    ||||||||  | |||||||| ||||| || ||||| ||||||||  | ||||| || ||||||||||| | |||  |||| |||||||| |||||||| |  |
---------gttagga-gattttcttctcaaagtgctcctaggagaatagcataatattttgtctgacatgttttgcgctc-caaagGCTGAACTTGAAGTTGAAAGGCTGGATCAGCTCAAAGCTAGTAGGATGAAGGATATTGCGTTCAAAAGGCAGACTGAACTTGAAGATATATATGCCCAGG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G101874_T01 (Zea mays), 3'ss of exon 7
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgct-aatattca--tgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
|| | |  || |  |||  |   |  | ||||  |||    |  |       |   || ||||  | ||| |  | |  |  ||||  |||||||||| || ||| | ||| | ||||||||||||   |||   |||||||||||||| |||||||||||| | ||||| ||||| || || ||| |||
gtgagtcttagta-attattttttggtgctatcacctgatatgaagtattcctttggcctgcttgacatttacttctccatattgttcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAATACAGCAAGATGAAAGAAATTGCTTTCAAGAAGCAAACCGAGCTGGAAGATATCTACGCTGGTG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G10090.1 (Glycine max), 3'ss of exon 7
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
      || || || ||     || ||   |         ||   ||  | |  || ||   |  |  |  | | |  ||  |||||||||| ||||||||||| |||||||| |||| ||||||   | |||||||||||||||| ||||||||||||  |||||||||||||||||||||  |||
-----gtagatggcttt--ctgatgtttacaaactagtgtttcacaaataatgcctactgaatttttcttgttttatgtt-atgaagGCTGAAGTGGAAGTTGAAAGGCTTGATCAGCAGAAAGCCCACAGAATGAAAGAAATTGCTTTCAAGAAGCAAGATGAGCTTGAAGAGATATATGCCTGTG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
||| |  | |      |||  ||| | |  ||     |||  || |     |||     |  |  | || || | | |    | |||||||| ||||||||||| || ||||| ||||||||||| ||| | ||||| |||||||| |||||||||||| | ||||| |||||||||| ||| ||||
gtactaaagaactt-ctga--aatttacggattcgagctccaagtatgatattaacttctttttctttttatttgata---ataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 6
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
||| |  | |      |||  ||| | |  ||     |||  || |     |||     |  |  | || || | | |    | |||||||| ||||||||||| || ||||| ||||||||||| ||| | ||||| |||||||| |||||||||||| | ||||| |||||||||| ||| ||||
gtactaaagaactt-ctga--aatttacagattcgagctccaagtatgatattaacttctttttctttttatttgata---ataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 6
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
|||  |  ||  | | | || ||  || |    ||   |   |   |  |  || |   || |  | ||| | ||| |    | |||||||| ||||||||||| || ||||| ||||||||||| ||| | ||||| |||||||| |||||||||||| | ||||| |||||||||| ||   |||
gtaggtactaaagaacttatgaagtttacagattcgagttccaagtatga--tattaactgttttt-ttcctttaata---ataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGTCTGTG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G43450.1 (Glycine max), 3'ss of exon 12
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatatt-catgtaaaat-ttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
                                |||   | ||  |   ||  |  ||| | || || || | |||   || || |||||||||| ||||||||||| |||||| | |||| |||||| | | | |||||||||||||| || |||||||||   ||||||||| |||||||||| | ||
--------------------------------gtcacatgttcca---caaatgatgcctactgatttttcttgttttatgttatgaagGCTGAAGTGGAAGTTGAAAGGCTTCATCAGCAGAAAGCGAACAGGATGAAAGAAATTGCTTTTAAGAAGCAAGACGAGCTTGAAAAGATATATGCCCATG

upper sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
                          ||||||    | ||       |   |   |||     |  | | |     ||  |  |   |  | ||| | |     |||  |||||||||||||||||||| |||||||| || |||||||| ||| | ||||| |||||||| ||||||| |||| ||||||| |||||||||| ||| ||||
gtatttggcttcagaacagtaatgcttaattttggcttcagaatagtaatgtttaatggataatgctggcagtttattcattttactttgttttccttttg---ttgctaagGCTGAGGTGGAAGTTGAAAGGCTTGATCAACTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAGGCAAGCTGAGCTCGAAGAGATATTTGCCCGTG

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|164098231|gb|EL993083.1|EL993083
EST:     GTGATTTGATTGAGCAG                         GCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAA
genomic: GTGATTTGATTGAGCAGgtaatttata ... atttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAA
EST: gi|164022934|gb|ES155542.1|ES155542
EST:     TCGATGAGGTCACTGTGCCAGGTGCTCTCGCACGTGATTTGATTGAGCAG                         GCTGAGGTGGAAGTTGATAGGCTTGACCAGCT
genomic: TCGATGAGGTCACTGTGCCAGGTGCTCTTGCACGTGATTTGATTGAGCAGgtaatttata ... atttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCT
EST: gi|124952649|gb|EL027903.1|EL027903
EST:     CGATGAGGTCACTGTGCCAGGTGCTCTTGCACGTGAATTTGATTGAGCAG                         GCTGAGGTGGAAGTTGATAGG
genomic: CGATGAGGTCACTGTGCCAGGTGCTCTTGCACGTGA-TTTGATTGAGCAGgtaatttata ... atttgtgaagGCTGAGGTGGAAGTTGATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
                           tgctaat  putative branch site (score: 2)
                              taatattcatgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA