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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattcaaaatgccatatgaacatctcttgatgcccttaaaagcttgaattgctttcttcttctctaatccgtttttccctttgttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG

Basic information

species Arabidopsis thaliana
transcript AT1G14400.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 3'ss of exon 4
--------gtgaattcaaaatgccatatgaacatctcttgatgcccttaaaagcttgaattgctttcttcttctctaatccgtttttccctttgttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG
        ||||     |  |   || | |   |  |   ||    | |   || ||    |   | ||||  |       ||| ||   | | ||||  |||||| |||||||||| || || || || || ||||||||||| ||||| || || |||| ||| || |  ||||| || |||||||| |||||||||||  
gacatctagtgagcagcagctttaatttca--gttacaatattttgtcagttgcctgtgagggcatattctaatgggcatagttcttaaatgttttatc-cagTCCCTGCTCTGTGATCCAAACCCAAACTCACCTGCAAACTCTGAAGCCGCACGCATGTTCAGTGAGAATAAGCGGGAATACAACAGAAGAGTGCGTGAAA

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgaattcaaaatgccatatgaacatctcttga---tgcccttaaaagcttgaattgctttcttcttct---ctaatccgttt--ttccctttgttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG
   |  |  | ||          | ||| | |    |||   | ||  | |  |   |     |        | |     | |  | | |    ||  ||||||| ||||| || ||||| || |||||||| || || |||||||| ||||| || ||||||||||| |    ||| ||||||||| |||| || || ||  
---agcttgagattggtcggcgtcttctttggcatttgcggctgaatacgtcgacgacaacgatgcgtagagcgagattatctaatacacggctttgatgcagTCTTTGCTGTGCGACCCAAACCCGAATTCACCAGCGAACTCGGAGGCTGCCCGCATGTACAGCGAGAATCGGCGTGAGTACAACCGGAGGGTACGCGAGA

upper sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgaattcaaaatgccatatgaacatctcttgatgcccttaaaagcttgaattgctttcttcttctctaatccgtttttc---cctttg---ttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG
| ||      |  ||    |   || |   ||  |||    | |||    || |    |      |  || | |||| ||   |   ||   ||  ||||||| ||||| || ||||| || |||||||| || ||||||||||| |||||||| ||||||||||| | |  ||| || || ||| |||| || || ||  
gcgagagtggatggcttcttcttcagcgtgtgcagccgaacacagcgatgat-gacgacgatgcgtgaaagctgtttctctaacacgtggctttggtgcagTCTTTGCTATGCGACCCAAACCCGAATTCACCAGCAAACTCGGAGGCTGCTCGCATGTACAGCGAGAACCGGCGTGAATATAACCGGAGGGTACGCGAGA

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|125006781|gb|EL079050.1|EL079050
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCT
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCT
EST: gi|124936145|gb|EL013074.1|EL013074
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCC
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCC
EST: gi|86077068|gb|DR372825.1|DR372825
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
EST: gi|301501590|gb|HO207130.1|HO207130
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
EST: gi|47831557|gb|CK121241.1|CK121241
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
EST: gi|125299202|gb|EL313287.1|EL313287
EST:     AGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
genomic: AGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCT
EST: gi|125041717|gb|EL113986.1|EL113986
EST:     ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAG                         TCCTTGCTCTGTGACCCTAA
genomic: ACCAGTGGAGTCCAATCTATGATGTTGCTGCTATACTTACCTCCATCCAGgtgaattcaa ... gttattgcagTCCTTGCTCTGTGACCCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagcttgaattgctttcttcttctctaatccgtttttccctttgttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG
                        ctctaat  putative branch site (score: 3)
           ttgctttcttcttctc  CT-rich tract
                                          tttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattcaaaatgccatatgaacatctcttgatgcccttaaaagcttgaattgctttcttcttctctaatccgtttttccctttgttattgcagTCCTTGCTCTGTGACCCTAATCCGAATTCTCCTGCAAACTCGGAAGCTGCTCGGATGTACAGCGAAAGCAAGCGCGAGTACAACAGGAGAGTGCGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA