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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG

Basic information

species Arabidopsis thaliana
transcript AT1G22410.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g42960.2 (Oryza sativa), 3'ss of exon 3
gatttgaaaaaaat---aatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattg--caaatcatctaatgttaattg--aaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
     |||||   |   | |  || |   | |   || |       || |    ||  | ||| | |||||  ||||| | |  |||   ||||      |  | ||||||||||  | || |||||||| || || || ||||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || |||||||
-----gaaaagtgtaccactgctgaaacggaactgtaacctttgttaaactagcgtcattttggactattggtcaaataaac--atgaacattgctgtgtttcacagGCTGAAGTACGTGCGTTCTTCGATGTCCATGATCAAGAAGGTAGCCACCCAGGAGGTATCCACCTGGAAATGACTGGGCAGAACGTGACTGAATGCATCG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g27230.1 (Oryza sativa), 3'ss of exon 4
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttt--tcttgtattattg-caaatcatctaat-gttaattgaaaatatat---agGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
       ||   ||  | |   ||     |  ||  || |    ||      ||    |   |   |||  || |    |||||  | |  |   ||| |||   |||| || ||  |||| |||||||| ||||| || |||||||| |||||||| |||||  | ||||| || |||||||| |||||||| |||||||||||||
-------aactgattgtttgacatgtaccttttaaaaatgttgtattctgcattcaggcccatgcaattatcagactgactaatcatgagcttgtaatctatgacagGCCGAGGTACGAGCATTCTTCGATGTGCATGATCAAGAAGGAAGCCACCCAGGAGGTGTCCACCTCGAGATGACTGGGCAGAACGTAACCGAGTGCATCG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G117707_T02 (Zea mays), 3'ss of exon 4
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaat-gttaattgaaaatata-tagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
 ||||  |    |   | |    ||  | ||  | ||   ||   | |  |     ||  ||  ||  | | |  |||||| || || |  | || ||  ||||||||||| | || |||||||||||||| || |||||||| || ||||| ||||| || ||||| ||||||||||| |||||||||||||||||||| |
-atttctactggagtgtttacacttgatctaggaacattccattctggccttccaactgataccat-accattgctctaatcgtgaactccatatctaacagGCTGAAGTGCGCGCATTCTTCGACGTGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTGAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G365160_T02 (Zea mays), 3'ss of exon 4
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattatt-gcaaatcatctaat-gttaattgaaaatata-tagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
  ||| |       | | |    ||  | ||  | ||   |    | |  |     ||  ||  ||| ||      ||| ||  | || |  |  | ||  ||||||||||| | || |||||||| ||||| || |||||||| |||||||| || ||  | ||||| ||||||||||| ||||| ||||||||||||||||
--tttcactggggca-tttacacttcatctaggaacattccgttctggcctcccaactgataccatttgctgtgactctgatcatgaactccatctctaacagGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCTGGGGGCGTCCACCTTGAAATGACTGGGCAGAATGTGACCGAGTGCATCG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G396212_T02 (Zea mays), 3'ss of exon 3
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgttaat-tgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
             |  |  |   ||  | | ||  | | |    |    |      |   ||| | ||  |  || |     |  || |  | || || |||| || ||  | || |||||||| |||||||| ||||| || ||||| || |||||  | ||||| || ||||| ||||||||||||||||| ||||  |
------------gttcttcttctttcttcttctgtcgacgtcgtactcctcaaa--ccaatatgaatgtgatacaccatgcatgcatatatatatttacagGCCGAGGTACGGGCCTTCTTCGATGTGCACGACCAAGAGGGAAGCCAGCCTGGAGGTGTCCACCTTGAGATGACCGGTCAGAACGTGACCGAATGCACGG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S36_31V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------------------gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
                                                                                                      |  |         |  | ||| |||   || |||   |  |   |  |    |  |   |  ||||     |  | ||    ||  |  |     |  |||  ||||| |  ||||||||||||||||| || || |||||||  ||| | |||||| ||||||| |||||||| || ||||| ||||| || ||  | |
gtgagcgtctctgcaaggccttttccaacctcaattcacaatcttattcgctgcttagtcttttctgggagtttaatgctatatttactttgcctagtctatgtctactgttggtttctattgaattcacattcta-tgatccggcactgaccttgctgacgcgttatgtttgacaacct---ttttgtctacgtggttcagGACGAAGTTAAGGCTTTCTTCGACGTGCATGAACAGGAAGGTACACACGCTGGAGGAGTTCACCTCGAAATGACAGGACAGAATGTGACTGAATGTGTGG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ08096 (Selaginella moellendorffii), 3'ss of exon 4
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgtt--aattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
                       | ||| |  |  ||   | |   | | |     | | | ||     | | |    || |||    |       ||  |||| ||  ||| ||||||||||||||| ||||| || ||||| ||||| ||||| ||  | ||||| || ||||| || ||||||||||||||||||||||
----------------------gtaagtctcttgacat--cgatcgcagctcccagcatttgtttccagagaactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTGACCGAGTGCATCG

upper sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcg-gttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
                   |   |   |  ||  | |  |||    |  |   | ||     |  | |  |||   | |  | ||          ||  |||| ||  ||| ||||||||||||||| ||||| || ||||| ||||| ||||| ||  | ||||| || ||||| || |||||||| |||||||||||||
------------------gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtc------catccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG

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|124923696|gb|EL001859.1|EL001859
EST:     CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTG                         GCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
genomic: CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttt ... aaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
EST: gi|125108319|gb|EL161298.1|EL161298
EST:     CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTG                         GCTGAAGTGAGAG
genomic: CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttt ... aaatatatagGCTGAAGTGAGAG
EST: gi|86015792|gb|DR311538.1|DR311538
EST:     CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTG                         GCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
genomic: CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttt ... aaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
EST: gi|301501700|gb|HO207240.1|HO207240
EST:     CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTG                         GCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
genomic: CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttt ... aaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCC
EST: gi|124991449|gb|EL063718.1|EL063718
EST:     CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTG                         GCTGAAGTGAGAGCTTTCTT
genomic: CCATTAAGGCTCCTTGTGGTCTCAAGACTCGTCCCTTTGACGCCATCTTGgtacgttttt ... aaatatatagGCTGAAGTGAGAGCTTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG
                                   tgttaat  putative branch site (score: 3)
                        aaatcatctaatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcggttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - aaaaaaa
- - - - - - - - - - - - - - - - tagcaaa
- - - - - - - - - - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatca