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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatctttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta...

Basic information

species Arabidopsis thaliana
transcript AT1G13060.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 3
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatctttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta
| |||||| ||| ||||||||||| ||||| || ||||| || |||||||| ||||| ||||||||||| ||||| ||||| || ||  | || || |||||   ||  |   ||  |  |||  | ||  |    | ||  |   || ||   | ||   | |   | |  |                           
AACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgt---tagatttcaacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcag---------------------------

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G102596_T02 (Zea mays), 5'ss of exon 3
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatctttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta
| | |||| ||| ||||||||||| |||||||| ||||| || |||||||||||||| ||||||||||||||||| ||||| || || || ||||  ||||| |  || | |   || |||      |     | ||  ||  |||   |||||     |    ||  |   |||| |    |                 
AACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGGAACCAAGgt-cagaagtcggcttcctttcaataatt----atctcttatgttgcccctttgcagggtggggctaacataggttcttttcag----------------

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 4
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatct-ttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta---
 ||||||||||||||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| || || |||||||| |||||||| || ||||||    |   | || |||       || | |    || |  |||   ||| ||   | ||||||   || ||      |   | |  |||  ||| |||    
GTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGGGATCAAGgtaatctat--gcaaccttgaaccttgtatattgcatggttgcttttgtctgttctgttatctttaggtcagtctcctgcaaaatttctgc--cctagtttccc

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatct-ttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta-
 ||||||||||| ||||| ||||||||||| |||||||| || ||||||||||| || |||||||||||||| || |||||||| ||||| || |||||||||      | | || |||          |||    || |  |||    || ||   | ||||||   || ||      | | | |  |||     | |   
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatc--tttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 4
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatctttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta-----
|||||||||||| ||||||||||| ||||| || ||||| || ||||||||||||||||||||||||||||| || |||||||||||| | || |||||||||    | |     | ||||    |   | || |||  |   |  |  || ||||  |   |  |    |      | |  | |  ||  |   || ||     
ATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGGCATTAAGgtaatgtatttttgttgttttc--tctaatttgcactcttt-ttcaggcctgtgatctacaataattatggaatgatttgatagtactg--gttctgctactgta

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|125023330|gb|EL095599.1|EL095599
EST:     GCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAG                         TGCCGTCTACATG
genomic: GCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACATG
EST: gi|124914850|gb|EH988724.1|EH988724
EST:     CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGGAATCTTGGAATTAAG                         TGCCGTCTACATGAGCTGGCAAACAAGAGGAG
genomic: CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACATGAGCTGGCAAACAAGAGGAG
EST: gi|116463327|gb|EG505919.1|EG505919
EST:     CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAG                         TGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
genomic: CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
EST: gi|116444339|gb|EG486931.1|EG486931
EST:     CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAG                         TGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
genomic: CTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
EST: gi|164098660|gb|ES032167.1|ES032167
EST:     ACAGAAATCTTGGAATTAAG                         TGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
genomic: ACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACATGAGCTGGCAAACAAGAGGAGAATCTCTGTTTCCGGAGCT
EST: gi|164145390|gb|ES126984.1|ES126984
EST:     TTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAG                         TGCCGTCTACA
genomic: -TGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaact ... tctatccaagTGCCGTCTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatctttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctct