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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggcattgtgaatcttgacagcatttctctctcaatgatgattccctctcttaatcttccgttcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC

Basic information

species Arabidopsis thaliana
transcript AT1G17290.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01630.2 (Glycine max), 3'ss of exon 4
--gtttgtggcattgtgaatcttgacagcatttctct----ctcaatgatgattccctctcttaatcttccgttcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC
   ||  | |  || | ||  ||      |||||| |     |||  |      || |    | ||  |   |||    ||||||| ||||||| || |||||| |||| |||| |||||| ||||  ||||||||||| |||||  ||||| |||| || |||||||||||||||||||| |
gtattaattgggttatcaaattttggcttatttctttgctattcacaggcagggccatgaaattattcttatttccatgtcagGGTGTCAAGGGCTTGCGTGATACAATAGCTGCTGGAATTGAAGAGCGTGATGGTTTTCCTGCCAATCCTGATGACATTTTCATGACAGATGGTGCAAGCC

upper sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G05130.1 (Glycine max), 3'ss of exon 6
--gtttgtggcattgtgaatcttgacagcatttctct----ctcaatgatgattccctctcttaatcttccgttcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC
   ||  | |  || | ||  ||      |||||  |     |||  |      || |    | ||  |   |||    ||||||| ||||||| || |||||| |||| |||| |||||| ||||  ||||||||||| |||||  ||||| |||| || |||||||| ||||||||||| |
gtattaattgggttatcaaattttggcttatttcattgctattcacaggcagggccatgaaattattcttatttccatgtcagGGTGTCAAGGGCTTGCGTGATACAATAGCTGCTGGAATTGAAGAGCGTGATGGTTTTCCTGCCAATCCTGATGACATTTTCATGACTGATGGTGCAAGCC

upper sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtttgtggcattgtgaatcttgacagcatttctctctcaatgatgattccctctcttaatctt-ccgttcttcc-------tcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC
                         || |   ||| |||  ||||    | |||  | |  ||| |||       | | ||| ||   ||  ||         |||||||||||| || || |||||| | ||||||| |||||| ||||| ||||||||||| ||| || |||| ||||| || ||| |||| ||||||||||| |
gcaatgattacacccccctctaccatgggattttgggaagtttgatgttaattcattttttatggtgagatgtcatatcaattttattgtatttttgtccacatcagGGTATCAAAGGATTGCGTGATACTATTGCTGCTGGAATTGAAGCTCGTGATGGTTTTCCTTCTAATCCAAATGACATTTTCTTGACTGATGGTGCAAGCC

upper sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S7_123V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------gtttgtggcattgtgaatcttgac--agcatttctctctcaatgatgattccctctcttaatcttccgttcttcct--cagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC
                    ||  | |  | ||| |  |   |  || || | ||   |   ||  ||||| | |  | |  | |  ||  | |   ||||||||||| |  |  ||||| |  ||||| |  || || || |||||||||||||| ||||| |||||| | ||||| || || ||||||||||||||||
ttcacgcctttagtaactttttcttagtttcgtgtacatcacctcaggatgtttcaaccggagaaaattccgttttctgagatgcgattgctgcatgcagGGTATCAAAGTCTGTCGTGAGGACATTGCAGCAGGTATTGAGGCCCGTGATGGTTTTCCTGCAGATCCTGAAGATATCTTTATAACAGATGGTGCAAGTC

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|116451787|gb|EG494379.1|EG494379
EST:     TCTGGACCCAAATTCCCGGGAGAGCGACTGGTGCTTACAGCCACAGCCAG                         GGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGAT
genomic: TCTGGA-CCAAATTCCCGGGAGAGCGACTGGTGCTTACAGCCACAGCCAGgtttgtggca ... tcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGAT
EST: gi|124934069|gb|EL011170.1|EL011170
EST:     TTCTGGACCAAATTCCCGGGAGAGCGACTGGTGCTTACAGCCACAGCCAG                         GGTATCAAGGGGTTACGTGATGCAATTG
genomic: TTCTGGACCAAATTCCCGGGAGAGCGACTGGTGCTTACAGCCACAGCCAGgtttgtggca ... tcttcctcagGGTATCAAGGGGTTACGTGATGCAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagcatttctctctcaatgatgattccctctcttaatcttccgttcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC
                               tcttaat  putative branch site (score: 3)
                        ttccctctcttaatct  CT-rich tract
                                 ttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggcattgtgaatcttgacagcatttctctctcaatgatgattccctctcttaatcttccgttcttcctcagGGTATCAAGGGGTTACGTGATGCAATTGCTGATGGAATCGAAGCCCGTGATGGTTTCCCTGCTGATCCTAATGATATATTCATGACAGATGGTGCAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG