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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

Basic information

species Arabidopsis thaliana
transcript AT5G42020.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
cgatattccaagctaatcata-gtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgt----tatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
     ||  || ||||| | | | |  |   |  |    |   |    |||| | |   |       ||    | |  |||   ||     | | ||||   ||||||||||||||||||| || ||||||||||||||||||||||| || ||||||||| ||   |||||||||||||||||||||   |||||||| |||||
-----ttttaaactaatgacatgccttttgtagttagttggtcgtcttgattatctggatagtgcactgtgattcatatttgactgaactgtctcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
--cgatattccaagctaatcatagtcaat-aacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatct-gcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
   | |  |  |    |  |||  || || | ||  | ||      | | | |||   |          |  |  | ||       | | |    ||    ||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||| ||   |||||||||||||||||||||   |||||||| |||||
attgttgatatatttcatgcatgatctatcagcacatttc----ctgtgagcttgcactgtaacttgcctatttatgactgagctgtatcacctcctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtg-atgttggtgctaaccttttgttgttatgatct----gcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
     ||  ||| ||     |  || |  | | |        | |    |  | | ||  || || |   |      |||    ||| || | ||       |||||||||| |||||||| ||||||||||| |||||||||||||| || ||||||||| ||   ||||||||| |||||||||||   |||||||| |||||
----tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgt-atcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
----------------cgatattc-caagctaatcatagtcaataacatgtgtcagaatggagggattgtt--ttag---tgtgatgttggtgctaaccttttgttgttatgat----ctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
                  |||  | |||||||||    || | |     |      |||      ||  ||  |||    | |  | ||| ||||||  | | | | || || |    ||   |||||||||||||||| || || || |||||||||||||| || || || ||||| |||||    ||||| || |||||||||||||  || ||||| |||||
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtct-gctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 4
---------------------------cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
                             |||     | || || ||    || || || |       |  |   |   || |  | |||||||  ||||  |  | | |  ||  |   ||| |||||||||||||||| || || || |||||||||||||| || || || ||||| |||||    ||||| || ||||||||||  |  || ||||| |||||
gtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaa--attctcctctgatgttaatgcttgctatgtctcctt-cgccttgc-cagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAGTAGAGCACTTGGCAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
-------cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
            |  |||     | | |  |||  |  | | |     |  |  ||| | |  | || || || |     || ||| ||||   ||  | |  ||||||||||| ||||| || || |||||||| ||||||||||| || || |||||||||||    ||||||||||||||||||||||  ||| |||| ||| |
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgat-gatcaattgggaagtaga----aaacttatgtt--cattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4
----cgatattccaagctaatcatagtcaataacatgtgt------cagaatggagggattgtttt-agtgtgatgttggtgc----taaccttttgttgttatgatctgc---gcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
     ||| ||     ||| | ||  ||  | |  | ||       || | || | | |   ||   || |  | |||  |      |      |    |||    |||     ||||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||||||||||   ||||||||||||||||||||||  |||||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTGCTCTTTGCACATTGAAAGAAAATTTACGAGAGGAAAGTTATTATACTGTGGATGCTCAAGGTTCAATTCTTTCCTGCAGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
                          ||   ||  ||| |         || | ||  |   |  | |   ||||| | |          | |   |||||||||||||| || || ||  | ||||| |||||||||||| | || |||||||||||| | ||||| |||||||||||||||  ||||||||| |||||
-------------------------gtactttg-atcaaagccttctccttttctttcttacagctcgaaactaacatct----------accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 4
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatg-atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
                                ||      ||  | |  || |  |  | |    ||  | | | |       ||  ||  | |   |||||||||||||| || || ||  | ||||| |||||||||||| | || |||||||||||| | ||||| |||||||||||||||  ||||||||| |||||
--------------------------------gtactttgatcaaagccttctccttttct----ttcttac-agctcgaaactgacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGCAAGCT

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|124732881|gb|EH824283.1|EH824283
EST:     GGTTCTCTCCACAAATGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: GGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|124719608|gb|EH811010.1|EH811010
EST:     AATGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: AATGGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|125237725|gb|EL251810.1|EL251810
EST:     GGTTCTCTCCACAAATAGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: GGTTCTCTCCACAAAT-GGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|124903498|gb|EH977578.1|EH977578
EST:     GGTTCTCTCCACAAATGGTGACACTCACTTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAG
genomic: GGTTCTCTCCACAAATGGTGACACTCAC-TTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT
                        tgctaac  putative branch site (score: 1)
     tgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - attccaa
- - - - - - - aatcata
- - - - - - - - - - - -caataac
- - - - - - - - - - - - - - - - - - - - - - - - - -gttttag