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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta...

Basic information

species Arabidopsis thaliana
transcript AT2G30710.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttg--ttcctgttaattggatgtgtctttggtgattgtttgagcttat-gacatgcacgtcctctccttacagaatcatgttaatta
 ||||| | || || ||||||||||| |||||||| ||||||||||| ||||| ||| | ||||| || | | |||| ||||| ||    ||||| |||||||   |    | |  |    |   | | ||   | | | |   | |  ||| | |   || |  || | | |  |       ||| || |  ||   ||   
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctag-aattatatctactgaaagaaagggaacttaaggatttagaggactattacaag--

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA12G05350.1 (Glycine max), 5'ss of exon 8
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagctt---atgacatgc-acgtcctctccttacagaatcatgttaatta
 ||||| | ||||| ||||||||||| |||||||| || |||||||||||||| ||||| ||||| |||||| |||||||| |||||||| | || |||||||   | || |||     ||    ||   |  | |  |  |   |  || | |||  ||   ||| |   | |  |  | |   |   | | ||| |  ||  
TCAAAGTTGCTTGATGGTATGCAAGACCATTACACATTCGCTCAACCTGGAATTCAGAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacctttttctaaggccttttgttttcctccaagcattgt--atagttttatgaaatttaaatgcctcactattttttattgatttggtaccatttctat--

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G13330.1 (Glycine max), 5'ss of exon 7
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatc-atgttaatta--
 ||||| | ||||| ||||||||||| |||||||| || |||||||||||||| ||||| ||||| |||||| |||||||| |||||||| | || |||||||     || |||      |  ||||  |       |  ||   | ||| | |||  ||   | ||||    |   |  |||  || |  ||   | ||   
TCAAAGTTGCTTGATGGTATGCAAGACCATTACACATTCGCTCAACCTGGAATTCAGAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacacttttctaaggacattttgttt-tcctccaagcattgtataattttatgaaattt--aaatgccttactattttttattgatttgataccattttta

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA15G03200.1 (Glycine max), 5'ss of exon 7
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcc-tgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta---
 ||||| | ||||| ||||||||||| ||||| |||||||| ||||| ||||| || || ||||| |||||| |||||||| |||||||| | || |||||||  || || ||  |||        | | ||  | |    | |    |   ||||     || |    | |   || |  | |     || | ||| ||    
TCAAAGTTGCTTGATGGTATGCAAGACCATTATACGTTTGCCCAACCAGGAATTCAAAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacttttttct--cttaccgaacctcagttttaggaaaatataactac-atttggctaaattattctctcactctatattaatgctctc-tcttatttcaca

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA13G42180.1 (Glycine max), 5'ss of exon 7
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgct--agcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcc---tctccttacagaatcatgttaatta
 ||||| | |||||| |||||||||| ||||| || ||||||||||| ||||| || || ||||| |||||| |||||||| |||||||| | || || ||||  || || ||   || ||||  | ||  |    | | |||    | ||||  |||  |||       ||| |     | |   |   ||      |||||  
TCAAAGTTGCTTGACAGTATGCAAGACCATTATACATTTGCTCAACCAGGAATTCAAAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGACGgtaacttttttctcaggcctgttgtttttcttcaagtatatct---ataattgcatgaatttaaagaccccacttttgaatatggatttggatatgcattaat--

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 5'ss of exon 7
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatg-tgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta
 ||||| | || || ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||||||| ||||| | || || ||||||| |  |||       || ||  |  ||||   || ||| |||  | | | ||       |  |  | |           | | | |       |||   
TCAAAGTTGCTCGATGGTATGCAAGACCATTATACATTTGCTCAACCAGGAATACAAAGACTCGTGTTTAAGCTGAAGGAATTGGTCCGACGGATTGATGgtatgcccttttgtcgatgatcaaggaaatttattgctgtttttcatcaatattactttcaacaattttccaagaaatagttcagaaagaataactaaac-

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ05322 (Selaginella moellendorffii), 5'ss of exon 6
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta
 | ||||| || ||| | || || ||||||||||| ||||| ||||||||||||||| | ||||| |||||||||||||| |||||  | || || ||||||| |  ||| | || ||   | | | ||    |      |    || ||                                                  
TCCAAGCTGCTCGACAGAATCCAGGATCATTACACTTTTGCACAACCTGGAATCCAGCGGCTTGTCTTTAAGCTGAAGGAGCTGGTTCGACGAATTGATGgtaagacctttccagttttcacttttaaaacaaacactcgtgctttgcttag------------------------------------------------

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ25625 (Selaginella moellendorffii), 5'ss of exon 6
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta
 | ||||| || ||| | || || ||||||||||| || || ||||||||||| ||| | ||||| |||||||||||||| |||||  | || || ||||||| | |||| | || ||   | |     ||  |  |  |  | ||| ||  || ||                                           
TCCAAGCTGCTCGACAGAATCCAGGATCATTACACTTTCGCACAACCTGGAATTCAGCGCCTTGTCTTTAAGCTGAAGGAGCTGGTTCGACGAATTGATGgtaagatctttccagttttcactt-----ttaaaactagcactcgtgctttgtttag-------------------------------------------

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|125232636|gb|EL246721.1|EL246721
EST:     AGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATG                         AACCTGTTTCAAGACACATGGAAGAGCATGGGCTAGAGTTTCTTCAATTTG
genomic: AGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttctt ... tatatactagAACCTGTTTCAAGACACATGGAAGAGCATGGGCTAGAGTTTCTTCAATTTG
EST: gi|86086042|gb|DR381801.1|DR381801
EST:     AATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATG                         AACCTGTTTCAAGACACATGGAAGAGCATGGGCTAGAGTTTCTTCAATTTG
genomic: AATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttctt ... tatatactagAACCTGTTTCAAGACACATGGAAGAGCATGGGCTAGAGTTTCTTCAATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttgttcctgttaattggatgtgtctttggtgattgtttgagcttatgacatgcacgtcctctccttacagaatcatgttaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcctctc