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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaaaacgtatttttttggttatcttgttttagtcctgtggtgtttcttagatgcagttttattaactgtttctgtaactgcag

Basic information

species Arabidopsis thaliana
transcript AT3G11170.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 5'ss of exon 3
GAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaaaacgtatttttttggttatcttgttttagtcctgtggtgtttcttagatgcagttttattaactgtttctgtaactgcag---
||| |||||||| || || || || |||||||||||||||||||||||||| ||||| |||||||| || |||           | || |  ||       ||||    | | ||||||    ||||  |  | ||| | | | ||  |  ||  |    
GAGGATTAGTCATAGGACCCATCATCAGAACCATGGACATGTTGAGAATGATGAATCATGGCATCCAgtgagttgt--tttctctgttcttatttcaggagtttataatttttgtgtttggatgatgaggaatcattgattttgtccatttctttaccag

upper sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 5'ss of exon 3
GAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagtc---------------aaaaacgtatttttt-----tggttatcttgttt-----tagtcctg-tggtgtttcttagatgcagttttattaactgtttctg-taactgcag
| | ||||| ||||| ||||||||||||||||| || || || ||||| ||||| || |||||||||||| |||               |  ||  || ||  |     ||   ||||  |||      | ||| |    ||| | ||   |     | || | ||||||  ||   | |||||
GCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCTgtacgtctcttgaatcgctgggagcaaaatagttggtcgaaatgagcatctgatttggaagcaatccagacattgtgtatttcgtattactctaattactgttgatgactattgcag

upper sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 5'ss of exon 3
GAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagt------------caaaaacgtatttttt--------tggttatcttgttt-----tagtcctgtggtgtttcttagatgcagttttattaactgtttctg-taactgcag
| | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||||                | | || || ||        |||   |||  |||      | ||   | || ||| |||  |||   | |  | | |||   || |   || ||
GCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCGgtaagtacatttgaccgctgggagcataattcttggagaaagtgggcgtctgatttggtagcattctaatagtttttgttacgtgcttctcttattattgtcggtggtttttgtag

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|124767154|gb|EH857284.1|EH857284
EST:     CTCACCACCAGAACCATGGACGTGTTGAGAATGACGAATCTTGGCATCCT                         ATGTCTGAGAAAATCTACAATACTTTGGACAAGCCG
genomic: CTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaa ... gtaactgcagATGTCTGAGAAAATCTACAATACTTTGGACAAGCCG
EST: gi|124933600|gb|EL010744.1|EL010744
EST:     ATGTTGAGAATGACGAATCTTGGCATCCT                         ATGTCTGAGAAAATCTACAATACTTTGGACAAGCCGACTAGATTCTTTAGA
genomic: ATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaa ... gtaactgcagATGTCTGAGAAAATCTACAATACTTTGGACAAGCCGACTAGATTCTTTAGA
EST: gi|125022466|gb|EL094735.1|EL094735
EST:     ATGTTGAGAATGACGAATCTTGGCATCCT                         ATGTCTGAGAAAATCTACAATACTTTGGACAAGCCG
genomic: ATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaa ... gtaactgcagATGTCTGAGAAAATCTACAATACTTTGGACAAGCCG
EST: gi|124834976|gb|EH919415.1|EH919415
EST:     ATGACGAATCTTGGCATCCT                         ATGTCTGAGAAAATCTACAATACTTTGGACAAGCCGACTAGATTCTTTAGA
genomic: ATGACGAATCTTGGCATCCTgtaagtcaaa ... gtaactgcagATGTCTGAGAAAATCTACAATACTTTGGACAAGCCGACTAGATTCTTTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCTgtaagtcaaaaacgtatttttttggttatcttgttttagtcctgtggtgtttcttagatgcagttttattaactgtttctgtaactgcag

- - - - - - - - - - - - - - -  CATGGA