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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC

Basic information

species Arabidopsis thaliana
transcript AT1G13060.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 5
gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
                            | | |||| ||      | |    ||       |   |    || || | | | |      ||| | ||  |||||  || |     |  |||| |||   ||||  ||| ||||||| |||||| | |||||||||||| |  | || ||||| || |||||||||||||| || ||||||||   || ||||
---------------------------gtaggttttatcttttatttacctcctt----ttatgttgctttgctgcttgcttatactgtgttacttacgtatgaacttccgc---ttttcagTTACCGCTATGTGATGCCAGTTGAGGAAGCTGCTGAGTTAGCAAGGCGGGCTATTTACCAAGCTACATTCCGTGATGGGGCAAGTGGTGGTTGTGTTAGC

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 6
gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
                                 || ||   | | || |    |||  | ||   | |||   |  | |  ||    |  |  || ||||     ||    | ||| |  ||||||   |||||  |||||||||| |||||| | ||  | ||  |  || |||| || ||||| ||||| |||||||| |||||||||||||||||||||
--------------------------------gttagttaaactttctat--ttaactatcacc-tataactcttct-gccaaatttcgttgacaaatttcc---ttgttatacat-actagGTACCGGTATGACCTGTCAGTTGAGGAAGCTGCTGAACTTGCTCGACGAGCAATTTATCATGCAACATTTCGTGATGGGGCCAGTGGTGGAGTTGCTAGC

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 6
gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttact--tgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
                                           |     |  ||    |   ||  |||       ||  |   |  ||   |  | || |  ||||   |  || |     ||||||  ||||||  |||||||||| |||||| | ||  | ||  |  || |||| || || || ||||| |||||||| |||||||||||||||||||||
------------------------------------------gttagttaaacttcctatttaa--ctatcacctataactcttctgccaaattttgttgacaatttccttgttgtacatctagGTACCGATATGACCTGTCAGTTGAGGAAGCTGCTGAACTTGCTCGACGAGCAATTTATCACGCAACATTTCGTGATGGGGCCAGTGGTGGAGTTGCTAGC

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
    ||  |||         |||  |||   ||  |||    ||    |  | |     |     |  ||| || ||| |     |     ||  | ||  || | | |||     |   || |||   ||||||||||| ||||| |||||| | || || || ||  |||| || || ||||||||||||||||||||||| |||||||||||||| |||
----gtgttttt-------gcatggtcagatctcatgt----attctgagtgttctgttct----ttaaatcatattattcttatatgttatttttcttgttgttgtcactcatggc---agATACCGTTATGATATGTCTGTTGAGGAAGCTGCTGAATTGGCTAGACGATCTATTTATCATGCGACATTCCGTGATGGAGCTAGTGGTGGAGTTGCAAGC

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S39_347V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------gtaagtcatttcccaaacaacatcttcatcgctt--ttgtcccaatctcaaaggctaaa-aaccaaaatcta-atgatgttagttaagcaaccgtttcatatttatgatt-ttacttgcatcat-cagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
                                        |   | |  ||   |       | ||  ||  ||  || ||   || |   |   || |   |||   | |  || |  | | ||  | |   |||   ||| | || || || ||    |  | ||| |  || |  ||||||||  | || |||||    ||| | ||  |  | || || ||||||||||| |||||||||||||| |||||||| || | ||| 
gtaattacacttaaaatccagatcaaggatctgtgaacatggtggacggttattatcttgattttttttcatttgattttcttgattttgtatcttagatggccattctttgcatcaactcatttctgtacttgttgactatgtttgtttgttgctcattttttacagCTTTAACTGGGATATGTCTATCGACGAAGCAGTAGAGCTTGCTCGTCGTTCTATTTACCATGCGACTTTCCGTGATGGAGCTAGTGGTGGTGTAGTTAGT

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|86079424|gb|DR375181.1|DR375181
EST:     TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAG--AGGAGATC
genomic: TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATC
EST: gi|116463327|gb|EG505919.1|EG505919
EST:     TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATC
genomic: TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATC
EST: gi|164197460|gb|ES015240.1|ES015240
EST:     TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGC
genomic: TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGC
EST: gi|164158867|gb|EL999127.1|EL999127
EST:     TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGC
genomic: TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGC
EST: gi|164108853|gb|ES130766.1|ES130766
EST:     CAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCGAGGA
genomic: CAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGA
EST: gi|164175183|gb|ES197776.1|ES197776
EST:     TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGG                         GTACAAATATGATATGTCAGTTGAAGAAGC
genomic: TTTTCAGTCGGTTCTGGTTCACCATATGCTTACGGTGTGCTGGACAGCGGgtaagtcatt ... gcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC
 atctaat  putative branch site (score: 3)
                       tttcatatttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatttcccaaacaacatcttcatcgcttttgtcccaatctcaaaggctaaaaaccaaaatctaatgatgttagttaagcaaccgtttcatatttatgattttacttgcatcatcagGTACAAATATGATATGTCAGTTGAAGAAGCTTCCGAGTTAGCAAGGAGATCAATCTACCATGCGACATTCCGTGATGGAGCCAGTGGTGGAGTTGCTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG