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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

Basic information

species Arabidopsis thaliana
transcript AT4G02840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattgga-atttgcttcgaaattttgag--atttctctttgttttcatgctcttcgatgtttgatttcgtatctggatt---ttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
           |  | |  || |  | ||||| |  |||        ||| | |||    |  |||    |||       |||||   |   ||| ||     ||| |     | |||    |||  |||||| ||||||||  ||||||||||||| ||  | ||||||||||||||||| ||| | || || ||||||||||| |
--------gtaagccagcatccccctgtttctcccctttccccctccattcgtttcagtctgctgattcgtttggtgcaattttcgcccgaatcggtgcggattttggcgcgggaattgcgcttttacagGTTCTTGATGAAGCTGAACAACGAAACGGTGACCATCGAGCTTAAGAACGGCACCGTCGTACACGGAACCATTACCG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                        | |  |||||  | | |||     || |       ||||   | || | ||| ||||||     || || | |  | |  ||||    |   |    ||||||| | |||||  ||||||||||||| |||||||||||||| |||||||||||  |||||||||| |||||||| |
---------------------gtctcacatcttcattctcattccgcgtttccct----ttttctcactttttttttttttcaa----tttgaagctaaaatgtgtat---aaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 2
------------gtatggtttctactcggattctctttatttcttcggtttaattgg--aatttgcttcgaaattttgagatttctctttgttttcatgctct----tcgatgtttgatttcgtatctggattttttc-gcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG-
             |||  | |||  | |  || | ||| |||  | |  ||  |      || || ||      |   |  | | |  || |||| ||  |||    || | || | ||    ||     | |   |  |||||||||| ||||| |||||||| ||||| || ||||| ||||| ||||| || || ||||||||||| |||||||| | 
tttttctctgctctatc-tctctctttgtttttttttttttttgttgcgttggtaaattgatctgtttatgtgctgctatgtattttattttttttattttctgggatcaaagtctaataatatacgaacactgcatgagcaggTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattgga--atttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                        | |  | |||  | | |||  |   ||| |||     |  |    ||| |  || || |  | | ||| || | |  |   ||| |    |   |    ||||||| |||||||  ||||||||||||| || ||||||||||| |||||||| ||  ||||||| || |||||||| |
---------------------gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtct---aaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
gtatggtttctactcggattctctttatttct-tcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggatt-ttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                | || ||| | | | | | |  |||  ||  | |||| |     ||||   |||| | |||  |||  ||   | | | || | ||    ||     | | | |  | |||||||| ||||| |||||||| ||||| || ||||| ||||| ||||| || || ||||||||||| |||||||| |
----------------gtttttctctttctttgttgcgttatctgttaattgcgt-----tttt---atttttttttcattttctgagat-caaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttt--tcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                                               | |||||   | |||| || |||    |||||||||| ||| |  |   ||| |  | || || |||      |  |||||||||||||||  | |||||||| || || ||||| ||||| |||||||| ||| |||||||||| ||||| || |
----------------------------------------------gtctgctt---atttttcagtttttctcttgttttcattctcattaactattgttgacctagcttgatacgaaatttcagGTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtttctactcggattctctttatttcttcggtttaat-tggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatt-tcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                                   |||| || |  ||||   | | | ||    | | |  |||   |||   |  | |    ||||  ||| |  ||  |   | |     ||||||| ||||||| |||||||||||||| || || |||||||| ||||| |||||| | |||||||| ||||| || |
-----------------------------------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataatttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S90_45V6.1 (Physcomitrella patens), 3'ss of exon 1
-----gtatggtttc-tactcggattctctt-tatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttc--gtatctggattttttcg-------cagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
     ||    || | | ||   | ||| || | | | |  |||||  ||     | | ||     |||   | ||    | ||  ||  |||| || |      |||||   | || ||    || | |       ||| |||||||||||| ||||||| ||||| |||||||| ||||| || || || |||||||| || || || || || |
gtgcagtgcctttcccttcttttactctgttgtgtatttcgggtttcgtttaggatagtttttccttttctggtttgtgatgtggattattgctgttggcgtgacgatttttgggatttgtgggttgttggtgggtccagATTTTTGATGAAACTGAACAATGAAACGGTTTCAATGGAGCTGAAAAATGGTACCATTGTGCACGGCACTATCACAG

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|125118423|gb|EL167152.1|EL167152
EST:     TGAAGCTCGTCAG                         GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
genomic: TGAAGCTCGTCAGgtatggtttc ... tttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
EST: gi|152034269|gb|BP823720.2|BP823720
EST:     CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCA-CATGAAGCTCGTCAG                         GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
genomic: CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCACCATGAAGCTCGTCAGgtatggtttc ... tttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
EST: gi|19877683|gb|AU238514.1|AU238514
EST:     CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCACCATGAAGCTCGTCAG                         GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
genomic: CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCACCATGAAGCTCGTCAGgtatggtttc ... tttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
EST: gi|86076061|gb|DR371818.1|DR371818
EST:     CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCACCATGAAGCTCGTCAG                         GTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG
genomic: CCCTAATTTTCTCCTCTTCTTCTTCATTCTCTCACCATGAAGCTCGTCAGgtatggtttc ... tttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG
                         gtttgat  putative branch site (score: 5)
                                            ttttttcgc  putative PPT
                                           atttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA