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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA

Basic information

species Arabidopsis thaliana
transcript AT1G07770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G018228_T02 (Zea mays), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                            |      |  | ||||| | | | |     | |||    | | | ||    | |      ||  |||  |  ||   || || | | ||| ||||||| |||||||| || || || |||||||| |||||||||||||| || ||  |  | ||||||||||| ||||||||||| || ||||| |||||||
--------------------------------------------------------------------------gttagtccaggctgctgtctctacaaaatctgattagagtttgtctgtacactttgaccccagtgctaactg--tgcctct-ttgactggtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCCCGCCGTAAGAATGTTGGTGGCAAGGTTCTAGGTTTCTTTTATTGAA

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 3
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaa-attgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                       ||    || |  ||   || |    || |    ||   ||| | | |||  |||    |  |   ||  |||  |  ||   || | |    |||| ||||||| |||||||| || || || |||||||| |||||||||||||| || |||||  | ||||||||||| | ||||| ||| || ||||| || ||||
----------------------------------------------------------------------gttagtccaatccgctgtctctataaaagc--tgattagagttg-tctgtacaatat--gaaaccagtgctaactg--tgcctctttgactggtgtgtagTTTGGCTACATCGTCCTAACAACTTCTGCTGGAATTATGGACCATGAGGAGGCTAGCCGTAAGAATGTTGGTGCCAAGGCTCTAGGTTTCTTTTACTGAA

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctc---gctaatggtattaatggattgaagctattaaattgt--gcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                          | | |  |||      ||   |  |  |   ||||      |   ||| |  ||    |    ||||   | |    ||| |||  |   ||||  | ||||||| ||||| ||  |||| ||||||||||| ||||||||||| || || || || || ||||| || ||||| |||||||| || ||||| || ||| 
--------------------------------------------------------------------------acttaagttgacagtagtgtggggaatttcgtagtgagtattgcctttgactcttagggtatttggttccattctgctgatgctcgtttcttgtttgtagTTTGGATACATTGTTTTGACAACATCTGCTGGAATTATGGACCACGACGAGGCCAGGAGAAAGAACGTAGGAGGAAAGGTTCTTGGTTTCTTTTACTGAT

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgt--gcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                         ||   |   |  || ||   |   |  ||     ||    |||   ||||  |   |    ||  ||       ||||   | | |  || |  ||||||||| ||||| ||  |||| || || |||||||| |||||||| || || ||||||||||||||||||||||| ||||| || || ||||| || ||| 
----------------------------------------------------------------------aacgatcaagcgttaatcctcctcaagaggatttcatgttaccgctgcttttag-gtatgaacctgaaatctgattgttgagtttttcatcttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S45_88V6.1 (Physcomitrella patens), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                   |||| |  |    |  |||| |  |  | ||| ||   |  || |         |||  | ||  |   ||||  |    |||      ||   | ||||||||||||||||| ||| |||| || || |||||||||||||| || || || || ||  | ||||| || ||||||||||| || |||||||| || ||| 
-------------------------------------------------------------------gtttctctactcttccgcat-cgctttcaaaatatagcttctatttcaagaaaataa-acccgtaagccgtatcgacttgttgttttggttttgtggtgcagTTTGGTTACATTGTGATGACAACGTCAGCTGGCATTATGGATCACGATGAGGCCAGGCGAAAGAACGTAGGAGGCAAGGTCCTTGGCTTCTTTTACTGAG

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                                      |    |   || | |  ||| |   | |||| ||  || |     ||| | | ||      ||  | || |      |  |||||||||||||| |||||||| |||||  | || || ||||| || || ||||| || |||||||||||||| |||||||| |||||||||||||||||| 
-------------------------------------------------------------------------------------gtttgattttgagagacgaatcg--atggcttggtgcaaaga--agtaacgattttctc---ttcgatctctg-----gctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

upper sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 2
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                                                                                      |    |   || | |  ||| |   | |||| ||  || |    |||| | | ||      ||  | || |      |  |||||||| ||||| |||||||| |||||  |||| || ||||| || || ||||| || |||||||||||||| |||||||| |||||||||||||||||| 
-------------------------------------------------------------------------------------gtttgattttgagagacgaatcg--atggcttggtgcaaaga--actaacgattttctc---ttcgatctctg-----gctcagTTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

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|124954114|gb|EL029237.1|EL029237
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTG
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTG
EST: gi|164225212|gb|EL986258.1|EL986258
EST:     ATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: ATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|125215239|gb|EL229372.1|EL229372
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACAT
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACAT
EST: gi|116414319|gb|EG456911.1|EG456911
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|152038400|gb|AV821952.2|AV821952
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|152038534|gb|AV827595.2|AV827595
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGNGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|164234909|gb|ES052728.1|ES052728
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGTTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|116409593|gb|EG452185.1|EG452185
EST:     GCGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|164145975|gb|ES090948.1|ES090948
EST:     CTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: CTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|124792455|gb|EH882134.1|EH882134
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTAC
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTAC
EST: gi|116414320|gb|EG456912.1|EG456912
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|86081408|gb|DR377165.1|DR377165
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|164137248|gb|ES021955.1|ES021955
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGC
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGC
EST: gi|86075131|gb|DR370888.1|DR370888
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|301502833|gb|HO208373.1|HO208373
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|164091195|gb|ES082895.1|ES082895
EST:     GACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTA
genomic: GACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTA
EST: gi|125327626|gb|EL341706.1|EL341706
EST:     CTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
genomic: CTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAA
EST: gi|164219539|gb|EL968388.1|EL968388
EST:     GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAG                         TTTGGTTACATCGTGCTGACTACATC
genomic: GTGTCAAGGAAATTGAAGGTTGGACTGCCCGTTTGCTCCCTTCTAGACAGgttcgctctt ... aattgtgcagTTTGGTTACATCGTGCTGACTACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA
                       tattaat  putative branch site (score: 2)
                                        tattaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctcttcttataaactttctagttacagtggccttatgaattataagatcaagatttggaaatgtttttgaatcactttgcatactgtcccgaaacatcaatagtagtagctttgtttaatgctcgctaatggtattaatggattgaagctattaaattgtgcagTTTGGTTACATCGTGCTGACTACATCTGCTGGCATTATGGACCATGAAGAAGCTAGAAGGAAGAATGTTGGAGGCAAGGTTCTCGGCTTCTTCTATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG