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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G43930.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
--------gtaaagccttatgct--------actagtacatccatg--ttcagaacttggagatataacacagaact-tgtttgtgtgggccggtc--agATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
        || | |  |||||          |||| |     |||   ||||| |  |   | |||     |  ||| | | | | | |  |   |  || | || ||||||||||| ||||||||||| |||||  | || ||| | || |||||||| || || || |||||||||||||| ||||| | ||||||||
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
-------------------gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaac---ttgtttgtgtgggccg-gtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                            | ||| |||   |    || ||||  | |||    ||  | |    | |   || ||  | |    |  || || | || ||||| || || |||||||| || ||||| || || ||| | || |||||||| |||||||| || ||||||||||| |||||||| |||||||
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctca-gttctta-cttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
----------------------gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                        ||   || ||  | ||  ||| |   ||| ||      |   |  || ||      || |||   |       | || |||| ||||||||||||||||||||||||||||| || || ||| | || |||||||| || ||||| || ||||||||||  || ||||| || ||||
aatgatttgcttattatcctccacaactactcatattgctcatac-tttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
-----------------gtaaagccttatgctactagtac-atccatgttcagaac---ttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                  ||    | |   |||||| ||     |||  |  |       || |  |  ||     |  || ||  | |    |  | || |||| ||||||||||||||||||||||||||||| || || ||  | || |||||||| || ||||| || ||||||||||| || ||||| || ||||
tcaaaataatttacttattatcctcctcaactactaatattgctcatactttgtgtacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
--------------------gtaaagcctta-tgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtc--agATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                    | |   |   | || | |  |   |  ||   ||| | |    || | |||||   | | |  |||| |    | | |  || | ||  |||||||||| ||||||||||| ||||| || || |||  ||  || ||||| || ||||| |||||||||||||| ||||||  ||||||||
cggctaaccctaatgggccggcagcccaacagtggtgccggcctacacacactcaca-cacatag-tctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------gtaaagccttatgctactagtacatc-catgttcagaacttggagatataaca---cagaacttgt---ttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                                                           | |||   |   | | || |  ||    |||||| | |||   | | | |     |||  ||       | | |  | |  |||| | ||| |||| ||||||||||| ||||| ||||| || || ||| | || ||||| || || || || || ||||||||||  ||||||||||||||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------------------gtaaa-----gccttatgctactagtacatccatgttcagaacttggagatataaca--cagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                                                                            || ||     |   |||  | ||  |  || || ||| || | ||  |  |    ||  ||     | | | |   |      ||| | ||||||||||||||||||||||||||||| ||| | || ||| | || ||||| ||||| || ||||| ||||||||      ||| || |||||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattca-gttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

upper sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------------------------------------gtaaagccttatgctactagtacatccatgttcagaacttgg-------agatataacacagaacttgtttgtgtgggc-cggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                                                                                      || ||     || ||||      |     ||| | ||||           ||   | |||||   || | | | |  |  |  |||| ||||||||||||||||||||||||||||||||||||| || ||| | |||||||||||||| || ||||||||||||||      ||| || |||||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG

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|301502274|gb|HO207814.1|HO207814
EST:     GCATCGTTAGTGATGGTGAAACAACATCACATTTTTTCACAGTATTGGAG                         ATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAG
genomic: GCATCGTTAGTGATGGTGAAACAACATCACATTTTTTCACAGTATTGGAGgtaaagcctt ... ggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAG
EST: gi|116473290|gb|EG515882.1|EG515882
EST:     GCATCGTTAGTGATGGTGAAACAACATCACATTTTTTCACAGTATTGGAG                         ATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAG
genomic: GCATCGTTAGTGATGGTGAAACAACATCACATTTTTTCACAGTATTGGAGgtaaagcctt ... ggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
                    atataac  putative branch site (score: 3)
                  agatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG