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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg...

Basic information

species Arabidopsis thaliana
transcript AT1G09770.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os04g28090.1 (Oryza sativa), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagt-cgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttgggg----atttggccttttagg
 |||||||| ||||| || |||||||| || ||||| || ||||| || || ||||| || || |||||||||||||||||||| || || ||||| |||||| || | | | |      |||  ||| | |   ||  || ||    | |  ||     ||| ||  ||   |||   ||| | |    | |  |  ||| |  
CAAGAACCAGTGGGCGCGCATCTCGTCCCTCCTCGTCCGCAAGTCCGCCAAGCAGTGCAAGGCCCGCTGGTACGAGTGGCTCGACCCCTCCATCAAGAAGgtatgtgcatatcc---cactccccctcgtgatctgtc-tgctctgttagag-ctgcatttcttgctcactgatttagatttagcgcatgaatgagtttttcaca

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: AC203535.4_FGT001 (Zea mays), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcg-tgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 |||||||| ||||| || |||||||| || ||||| || ||||| || || ||||| || || |||||||| |||||||||||||| || ||||| |||||||     || |||| | |        |             |||  | |  |   |   |    ||  |    || | |    |  ||| || ||    |
CAAGAACCAGTGGGCGCGCATCTCGTCGCTGCTCGTCCGCAAGTCCGCCAAGCAGTGCAAGGCCCGCTGGTATGAGTGGCTCGATCCGTCCATCAAGAAGgtaaccgactgctcgcctctcttacggttctgtcttcctctctcggcagactagcctcactgcc-cggtcgccgttctatcactgattttcgctttgcttg

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv14s0036g00500.t01 (Vitis vinifera), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 |||||||| |||||  ||||||| |||||||||||||| || || || || ||||| || |||||||||||||||||||| || || |||||||| ||||| |||   |||    ||||  || | ||       |     |   |  ||| | | || |||       | ||     |||   | || |  |    ||
GAAGAACCAGTGGGCCAGGATCTCTTCTCTTCTCGTTCGCAAATCGGCCAAGCAGTGCAAGGCTCGCTGGTACGAGTGGCTTGACCCTTCTATCAAGAAGgtcagtttagttttttttttttttgtttttttccccaacaccctccaggaaaattttgaactgaatgctgtgttaaatcttgttaagttagtttacccgg

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ17718 (Selaginella moellendorffii), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 ||||| || ||| || | |||||||| || ||||   | ||||| || || ||||| || || || |||||||||||||| |||||||||||||| ||||| | |||  |||   ||       ||||  ||    |  || | |         | |                                          
CAAGAATCAGTGGCCTAGAATCTCGTCCCTGCTCGCCAGGAAGTCGGCCAAGCAGTGCAAGGCGCGATGGTACGAGTGGCTGGATCCATCTATCAAGAAGgtgaatcgacttcctcttccttgcttcttttctcacgg-atttgcatttgtctgctag------------------------------------------

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ16393 (Selaginella moellendorffii), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 ||||| || |||||| | ||||| ||||| |||||  | ||||| || || ||||| || |||||||||||||||||||| |||||||| ||||| ||||| |||||  | | |  || |||    ||  ||  |  | |   | |     ||                                              
CAAGAATCAGTGGGCTAGAATCTCCTCTCTACTCGTCAGGAAGTCCGCCAAGCAGTGCAAGGCTCGCTGGTACGAGTGGCTGGATCCATCGATCAAGAAGgtgagtcgaatcc-ctcttccctggattt--ctttttatctcacagatttgcctgccag-----------------------------------------

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ17860 (Selaginella moellendorffii), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 ||||| || ||| || | |||||||| || |||    | ||||| || || ||||| || || || |||||||||||||| |||| ||||||||| ||||||| |||  |||   ||       ||||  ||  | |  || | |      ||                                              
CAAGAATCAGTGGCCTAGAATCTCGTCCCTGCTCCCCAGGAAGTCGGCCAAGCAGTGCAAGGCGCGATGGTACGAGTGGCTGGATCTATCTATCAAGAAGgtaaatcgacttcctcttccttgcttcttttctcatgg-atttgcattttgcctgccag-----------------------------------------

upper sequence: AT1G09770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ17861 (Selaginella moellendorffii), 5'ss of exon 1
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg
 ||||| || |||||| | ||||| ||||| |||||  | ||||| || || ||||| || |||||||||||||||||||| |||||||| ||||| ||||| |||||  | |        |||| ||  | |  |  | |||           | |||||||     | |||   ||   |                  
CAAGAATCAGTGGGCTAGAATCTCCTCTCTACTCGTCAGGAAGTCCGCCAAGCAGTGCAAGGCTCGCTGGTACGAGTGGCTGGATCCATCGATCAAGAAGgtgagtcgaatcc------ctcttccctggatttctttttttc---------tcacggatctg-----cctttccctgccag------------------

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|125086847|gb|EL146184.1|EL146184
EST:     AACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAG                         ACTGAATGGAACCAGAGAAGAAGATGAGAAGCTTCTAC
genomic: AACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtg ... gttaatgtagACTGAATGGA-CCAGAGAAGAAGATGAGAAGCTTCTAC
EST: gi|125093375|gb|EL150976.1|EL150976
EST:     CCATCTATCAAAAAG                         A
genomic: CCATCTATCAAAAAGgtaagtcgtg ... gttaatgtag-
EST: gi|125093375|gb|EL150976.1|EL150976
EST:     CCATCTATCAAAAAG                         A
genomic: CCATCTATCAAAAAGgtaagtcgtg ... gttaatgtag-
EST: gi|124998985|gb|EL071254.1|EL071254
EST:     CAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCAATACTATCAAAAAG                         ACTGAATGGACCAGAGA
genomic: CAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCA-T-CTATCAAAAAGgtaagtcgtg ... gttaatgtagACTGAATGGACCAGAGA
EST: gi|125198869|gb|EL213823.1|EL213823
EST:     CGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAG                         ACTGAATGGACCAGAGAAGAAGATGAGAAGCTTACTACATCTTGCTAAACT
genomic: CGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtg ... gttaatgtagACTGAATGGACCAGAGAAGAAGATGAGAAGCTT-CTACATCTTGCTAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAACCAATGGGCTCGGATCTCGTCTCTTCTCGTTCGTAAGTCTGCTAAACAGTGTAAAGCTCGCTGGTACGAGTGGCTCGATCCATCTATCAAAAAGgtaagtcgtgttcgcgttttccttctcttaactagtagtgttcgaaaaaaaactatggatctggcgaacatttttttgtttggggatttggccttttagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa