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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatgttactaatactgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC

Basic information

species Arabidopsis thaliana
transcript AT4G38040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
-gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatgttactaatactgttaaatggtggtgtta-cagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
   |||   |           |  || |  |||| |  | | || | |  |  ||   |      |||  || |  || | ||   |  |  |   | |||||| |||||||| ||||||||||| ||||| ||||| || ||| ||||||| || || |  || ||||| || ||||||||||||| |||    ||||||
cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattt-tattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC

upper sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G33330.1 (Glycine max), 3'ss of exon 3
------gtaaactaagtcctccctcttttatta-ggaactctggtagatcctggagttgtattgttggctcaatgttactaatactgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
      |       | |  | | |  ||| ||  | ||      ||||   |||   |   || |||  ||        | ||| | |||     || | || |||||| |||||||| || |||||||||||||| || ||||| ||  | ||||| ||||| | |||||||||||| |||||||| ||||||||||||||||| 
actgatgatggtgcaatgatacgtagtttgttctgtaagatcaatagacaatggttctac-ttattgattctgaaaatttgataatttta-----tgcttttgcagGACTACTCTTGGATTCTGGGCTGGTCATCGGAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT

upper sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G02630.1 (Glycine max), 3'ss of exon 3
gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatgttactaata--ctgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
 | |   ||          ||| ||  | ||       ||| |  ||| |    |||     | | || | || | |   || |||||    |  || ||| || |||||||| |||||||| |||||||| || ||||| ||  | ||||| ||||| | |||||||||||| |||||||| ||||||||||||||||| 
atgatgcaataatatgtagtttgatctgtaagatcaacaga-caaggattctacttgcatatttattgattctgaaaatttgataaatttgtgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT

upper sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0218g00090.t01 (Vitis vinifera), 3'ss of exon 3
----gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgta-ttgttggctcaatgttactaatactgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
     |        | |  |   ||  ||       |   || |||       |   | || |  | | | ||   |||| | ||  | | |      || |||||| |||||||| ||||||||||||||||| || || || ||  | |||||||| || | ||| ||||| || ||||| || ||||| |||   ||||||
tagcatgtttctcatacaacgaattgaatgtaagttttatgtggatggaaagatcccagttatgagattattgc--ctaaaattg--agaagcatactttgcagGACAACTCTTGGCTTTTGGGCTGGTCATCGGAACTCCAAAATTAGAGTTATACTAGCACGTGTATGGGAGAATGACACTGAACTTGACATTATGAACAAC

upper sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatg---ttactaatactgttaaatggtg-gtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
||   |||     |     |  | | |  ||  || | | ||    |||||  | || |  ||| |||   | |  | |  | ||||   |||  |  | |||||| || ||||| |||||||| || ||||| ||||| || ||| | |||||||| || | | | ||||| || |||||||||||||||||   |||||||
gtttgctatagttttttcttaatttaataaatgcttgcaaatt---gagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC

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|125108079|gb|EL161145.1|EL161145
EST:     TGCTCTCCCTGCTGGTGGAAATGATTTGTTGAGAATCG                         GACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
genomic: TGCTCTCCCTGCTGGTGGAAATGA--TGTTGAGAATCGgtaaactaag ... ggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
EST: gi|163971347|gb|ES025151.1|ES025151
EST:     GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCG                         GACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
genomic: GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCGgtaaactaag ... ggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
EST: gi|86063895|gb|DR359652.1|DR359652
EST:     GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCG                         GACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
genomic: GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCGgtaaactaag ... ggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
EST: gi|86063894|gb|DR359651.1|DR359651
EST:     GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCG                         GACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT
genomic: GTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCGgtaaactaag ... ggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagttgtattgttggctcaatgttactaatactgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC
                         tactaat  putative branch site (score: 1)
                            taatactgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatgttactaatactgttaaatggtggtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT