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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaaaaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC

Basic information

species Arabidopsis thaliana
transcript AT1G79530.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 10
gtacacaaaaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatct-gagct--gtggttttttgatcaagt-agGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC
                 | | |   || |       |  ||  | | |   || ||| || | |  ||   ||||||     |   || ||||||| || ||||| || || || |||||||| ||||| || || ||||||||||| || |||||| | ||||| ||||| |||||||| || || ||  
----------------gtagctgaagccaaaggcacaccatgtttagtttagactcaaattttgcacttactggtttcactttattgtcagGCTGTTGGAAAAGTCCTGCCTGAGCTGAATGGAAAACTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGATTTGACATGCCGGA

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
gtacacaa-aaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC
|||||  |   |   |||  |  ||   | || |   ||| ||     | |   || | ||  |   |||   ||| | |      |||| || || ||||||||||| || || ||||||||||| || || ||||| ||||||||||| ||  | ||||||||||||||||| || ||||| || |
gtacaagatggatggacacag--attttatgcttactattttcagtgctggtatatgagattgggtttgt---tttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
gtacacaa-aaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC
|||||  |   |   |||  |  ||   | || |   ||| | |   |  || | |  |   |  | |   ||||| |||      ||||||| || |||||||||||||| || ||||| ||||| || || ||||| |||||||| || ||  | ||||||||||||||||| || ||||| || |
gtacaagatggatggacacag--attttatgctttctatt-ttcagtactggtatttgtgattaggttt--gttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 10
gtacacaaaaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC
|||     | |   |  |  ||  |       |  |||      || | |   |   | |      | ||  | |||| |    |||||||| || ||||| ||||||||||| || || || || || |||||||||||||| || |||||| | ||||| ||||| ||||| |||||||||||||
gtatg---agatggatttaattcacatggaagtagaatcccataaagttgtacaaggtgt---gattttgactgtttggtatcatagGCTGTTGGAAAAGTCCTTCCAGAACTCAACGGAAAGCTCACTGGAATGGCCTTCCGCGTCCCAACACCTAATGTCTCTGTTGTGGACTTAACTTGTCGAC

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|125101696|gb|EL156728.1|EL156728
EST:     TCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG                         GCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCC
genomic: TCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAGgtacacaaaa ... gatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC
                                       ttttttg  CT-rich tract
                                       ttttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacaaaaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA