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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctattatcatttcaccattagtctttcccatagttgcatcgtttcgttttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG

Basic information

species Arabidopsis thaliana
transcript AT5G20890.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------gctattat-catttcaccattagtctttcccatag---ttgcatcgtttcgt--tttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG
                                                                     | || ||   |||   ||  ||   |  |  | |    || |||  |  | |  |||   |   |  | |||| |  | ||    | ||||  ||  |     ||||| || || ||||||||||| ||||| ||  | || ||| ||||||||||||| ||||| || ||||||||||||||
gtactgaaattgttaatgctttatactatatatttgcagttagttgttttgaacttttgatttgtgactgttactacatattctgccgctatattgccttaaatacttttcattataccatcatttaagtcactgca-gattctgatttgtg--tgtgctactactgaattgcagGGCAGTACCAACTTGGAAGCAATTCAAATTCTTAAGAAAACTGGAGGGTCTCTAAAGGACTCCTTTTTGGATGAAGG

upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 7
---------------------------------gctattatcatttcaccattagtctttcccata-gttgcatcgtttcgttttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG
                                   |||  |  | |  | | || | | ||    | | ||  |  |   |||| |  |||| | |||||  |||||| |   |     |  | |  |   ||||| ||||||||||||||||| ||||| ||  | || | ||||||||| || || ||||| || ||||||||||||||
gtattcacagggttgagtggaagttggtgttgaaatatcttgttattgcaactactatatctgggatgctgtctgatgatgttt-gtgttgtcacatgatgcttttctaatgattgatatgcaccactgtgcagGGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG

upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------gctattatcatttcaccattagtctttcccatagtt-gcatcgtttcgttttggattgttatatgatttttttctgacatt---ctgcttttatc----gttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG
                                                                  ||| | | |     |  ||| |    |||| ||   | |   ||  |  |  |||||||  |||  | || |   |||   | | || ||||          ||||| ||||| ||||||||| ||||||| ||  | || ||||||||||| ||||| |||||||| |||||||| |||||
gtatacaaatagcttaattaaagttggttatcatttacattaaactttgatatgtttatctgtataattttaactcttgaaaaagtgtggttcatacttcatagcaactcagtc-gtgttgttattcgatggtgttatagtattgatcggtttctatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTCAAGGATTCATTTTTGGACGAAGG

upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 15
---gctattatcatttcaccattagtctttcccatagttgcatcgtttcgtt-ttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG
       ||   |    |    |  |  |||  |    |   || | | ||| || ||| ||  |||| | ||| |  |   ||  | | | |  | |   ||||| ||||| ||||||||| ||||||| ||  | || ||||||||||| ||||| |||||||| |||||||| |||||
ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattgg---tttcgatctgaatggt-ggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG

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|124774491|gb|EH864620.1|EH864620
EST:     AATGGCCGTGGATGCTGTTTTCAGGCTTAAAG                         GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTC
genomic: AATGGCCGTGGATGCTGTTTTCAGGC-TAAAGgttccatttc ... cgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTC
EST: gi|116444514|gb|EG487106.1|EG487106
EST:     ACAAGGAACATTTTGCAGAAATGGCCGTGGATGCTGTTTTCAGGCTAAAG                         GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCT
genomic: ACAAGGAACATTTTGCAGAAATGGCCGTGGATGCTGTTTTCAGGCTAAAGgttccatttc ... cgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG
                         ttctgac  putative branch site (score: 2)
                                      cttttatc  putative PPT
        attgttatatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctattatcatttcaccattagtctttcccatagttgcatcgtttcgttttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - -ttcacca
- - - - - - - - - - - tctttcc
- - - - - - - - - - - - - - - - - - - - - - - gttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttt