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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG

Basic information

species Arabidopsis thaliana
transcript AT5G49820.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 5
------------------------------gtagttttatcatcttttatcactcataattgct---attcgatttcaatgttattgttggtct-ttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
                               ||   |||  ||   || |     | | || ||   ||      |   |||   ||    | |  |||   ||||| |  | | |   | |||||  ||  ||||||||||| || || |||||||| || || |||||||| ||||| || || | ||| ||||||||||| || ||||| || ||||| ||||||||  |||
gtttgacctagcggtttactgtgacgagtcctaacattaatatggcttgtttgataaagttactgtaatgaaccctttttgtacctgcaaatgtactgaagattgttctact-tgatgaaattgttacatt-cagAATGTTGCTGCTGTTACATCAACCTCGACCCGTACACCAATCTACAAGGCATATGCAAAAGGAGAAAATATTGGAGATGTCACTGCCAAAGGAGAAAGTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 5
gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgta------tcaatcatt-tgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
||  | |  ||| |   | |  |  |  |    |||| || || ||   |||   |    ||  |    | ||  || |      ||  || || ||   | |   ||||||| || || || |||||||| || ||||| || || || ||||| |||| ||| | |||||||||||| ||||| || ||||||||||| || | ||
gtc-tgtcctcaccagctgttgcaaaccacacatattggacttaaaatatatctatctgtttcaaaaagtattgatgaagagcgttctttctttctgcaatgttctagAATGTCGCGGCTGTTACATCAACATCAACTCGAACTCCAATTTATAAGGCCTATGCAAGAGGAGAAAACATTGGAGATGTCACTGCTAAAGGCGAATCTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 5
--gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
   |  | | | || |     |   |   |||||   ||| |||| ||    |||| |       ||   |  ||| ||| |||      ||    ||  ||||| || || || || |||||||| || ||||| || || |||||||| |||| ||||| ||||||||| || ||||| || ||||||||||| || | ||
gtttgctctcaccagcaccagtattttcaaattggacttc-attttaacagcattggtaaa----gaacatcctttctgtttca------tgcaacat-gcagAACGTCGCTGCTGTTACATCAACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 5
--------------------------------gtagttttatcatcttttatcactcataattgctattcgattt-caatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
                                    | ||   ||  | | | ||| ||| ||   | | |  || |||  |   || ||   | |     || |  |||| | |  ||||| | |  |  ||||||||||| || || || || || |||||||| ||||| || || || || | ||| |||||||||||||| || || || ||||||||||||||  |||
gtttgtcctactgatttgttgcaacttgcaacaggttcttgctatagtatgttactaatatttttaacttgccttgcaaaatgggtgatgaaatgta----ttctacttgtttgatgcattt-tctcctatcagAATGTTGCTGCTGTCACTTCCACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 3
--------------------------------------------gtagttttat-catcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgtttt--atcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
                                             ||  | |||  || | |    |   |||  |     |  || |  || |   | |   | |    |      |   |  | | |  ||  |||    || ||||||||||| || ||||||||||| || ||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||||||||| ||||
gttttactcattacttctttctttctgctcactcattcacttatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatcaactcagcagtgcagccttatttcttcatttctgctctcagAATGTTGCTGCCGTAACATCAACCTCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAACATAGGGGATGTCACTGCTAAAGGAGAATGTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 2
-gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
  ||| ||| |    |    ||  || |     ||   | | | | |    | | |           |||| ||||  | |   |    | | |  || ||||||||||| || ||||||||||| || ||||| ||||| || |||||||||||||||||||||||||| ||||| || || |||||||||||||| ||||
gttaggtttgtttgttgacttctttc-tgccgactcaccaactgctaatgaactctgcagtgcaagctttttttttaatttttttttcatttctgctctcagAATGTTGCTGCTGTAACATCAACATCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAATATAGGGGATGTCACTGCTAAAGGAGAATGTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 5
gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
   |||| ||  | || |   | | ||    | |||  | | |||| ||||    || |  || || |||||             |||||||| ||   |||||||||| || ||||| ||||| || || || ||||| || || |||||||||||||||||||||||||| ||||| || |||||||||||||| ||||
---gtttgatggttttct--taat-atgccaggtatatgttgtcaa-gttaccactgctgcttcatatttgt-------------atttgtttaattgtagAATGTTGCTGCGGTAACGTCAACATCAACCCGCACACCAATTTACAAAGCCTTTGCTAAAGGAGAAAACATTGGAGATGTCACTGCTAAAGGAGAATGTG

upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32878 (Selaginella moellendorffii), 3'ss of exon 5
gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatca-tttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
                                              |||| ||       |||  | ||| || |        |   ||| || | || ||||| ||||| |||||  | || || || |||||  |||| || || || ||||||||     |||||||||| |||||| ||||||| |||||||||||| 
---------------------------------------------gtgttcttaccttgttttattatttcttctcaagaggcttggttttttctttcgcagAACGTTGCTGCAGTGGCGTCTACTTCGACTCGAGCACCCATATACAAGGCCTTTGCGCGTCGAGAAAACATTGGAGACATAACTGCAAAAGGAGAGTGTA

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|86038682|gb|DR334437.1|DR334437
EST:     CAGTTCCACATCTTTTTCTTCCACTGGCTTGTGCTGCTAATGTTGTTAAG                         AATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCC
genomic: CAGTTCCACATCTTTTTCTTCCACTGGCTTGTGCTGCTAATGTTGTTAAGgtagttttat ... tttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG
             ctttgat  putative branch site (score: 5)
                                        tttgtttt  putative PPT
              tttgatttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttatcatcttttatcactcataattgctattcgatttcaatgttattgttggtctttgatttttgtttttgtatcaatcatttgttttatcacagAATGTTGCAGCAGTAACATCAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA