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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA

Basic information

species Arabidopsis thaliana
transcript AT5G52920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 4
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgcc--gcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                                                   | | |  |  | ||| |  ||    | || |||     |  ||  | |||  |  | |||||||   |  ||||| ||||| ||||| |||||||| ||||| ||||||||  |||||||||  ||||| ||||| ||||||||||||||||||||||| || || |||||| |
---------------------------------------------------gtaatagtcaacattcatttcactga-atattata--aacactcttgtttcattctcattttctgaacttgcagACAAGGATTGGGATGATATTAAGTTTGGTGTGGAGAATCAAGTTGACTACTATGCCGTTTCTTTTGTCAAAGATGCTCAAGTTGTGCATGAATTGAAGGA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                                          |   | || |    |   | | |||  ||||    ||||| |     ||     | |||  ||    |||        |||| ||||||||||| || ||||| ||||| ||||| ||  ||||||| |  ||||| ||||||||||| ||||||||||||||||| |||||  | ||| |
------------------------------------------gtaatagtcg----gcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 4
-------------------gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaat-----tattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                    | | ||| ||     | | ||  | |  | || ||  |||  || | ||||    |  |  || ||      ||  ||| |||   ||        |     ||||      |||   |||  ||||||||||| ||||| ||||| || ||||||||||| |||||||||||||||||||| ||||||||||| || |||||| ||||||| || ||| |||||||
gtcagaattcagattattgatcccaatcttgacgatgctctggtgtctatttctttgtgtgcctctagttgtgtgggagggtagttgctcaggattgatgttatggtggcttcctatggacataatattcacattaatttgttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTTTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAGCTGAAGAA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 4
-------------------gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaat-----tattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                    | | ||| ||     | | ||  | |  | || ||  |||  |||  ||||    |  |  || ||      ||  ||| |||   || |      |     ||||      |||   |||  ||||||||||| ||||| ||||| || ||||||||||| |||||||||||||| ||||| ||||||||||| || |||||| ||||||| || ||  |||||||
gtcagaattcagattatgaatcccaatcttgacaatgctctagtgtctatttctttgtgtgccttgagttgcgtgggagggtagttgctcaggattgatgttatggtggtttcctatggacataatattcacattaatttgttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
------------------------gttcgaattttctgtttaccctctttttcactttttcttgttgctttg------gttgaagtgttgcatatttaagtctga---aagatctta-----ctctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                         |    ||| | | |||      || | || || ||||   ||| |         ||   ||  || | |  |  ||  |    ||| | ||       ||  | |   || |  | |   | ||   ||||  |||||||||| ||||| || || |||||||||||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||| || || ||  |||||||
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactg-acaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
------------------------------gttcgaattttctgttt---accctctttttcactt---tttcttgttgctttggt-----tgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                              | | |  ||||   |||   ||| | | ||  || |   | ||    || || |||       ||  | ||   ||| | || |    | | |  |   ||    || | |||||  | ||||    ||  |||||||||| ||||| || || |||||||||||||| |||||||||||||| ||||| ||||| ||||| || ||||| ||||| || || ||  |||||||
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgattt----gctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G24270.1 (Glycine max), 3'ss of exon 4
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAA-GTTGTACACGAGTTGAAGAA----
                                                  |||| | ||| || ||  ||   ||||  |  ||| ||             |  ||||| |           |||||||| || || || || |  ||||||||||| |||||||||||||| ||||  ||||||||||| || |||||  || ||||| || ||  |||| ||    
-------------------------------------------------gtgaatt-ttgaatgttagagg--gaaaagtgctacacta----------ccttcaattact-----------gagaagGATTGAGATGACATCACGTTTGGAGTGGATAACAAAGTTGACTTATATGTTGTTTCCTTTGTTAAGGATGCCAAAAGTTGTTCATGAACTGAAAAATTAT

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 4
gttcgaattttctgtttaccctctttttcactttttcttgttgctt-tggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattatttt--cttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                                       ||||    |||    |||     || ||||   |  |||    ||  | ||    | |   |    | ||  |||   |||| ||||| ||||||||||| ||||| || ||||| || || || ||||| |||||||||||||| |||||||| ||||||||  |||| || || || ||||||||
---------------------------------------gttggacatggaatgagtccccaatgtttatagc--aaatgctttgttttgcaattcaaaataacaatttgctttgatttgctgcagAAAAGGACTGGGATGATATCAAGTTTGGTGTTGACAATAAAGTGGACTTTTATGCAGTCTCCTTTGTTAAAGATGCAAAAGTAGTCCATGAATTGAAGAA

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatct---tactctgatgcttattttt------tgtaattattttcttgccg------cagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
||  |   ||| | | |   |   |     | | |   | || |||| ||||   | |    |||||| | |||   ||| |    |||| |  ||||  | ||      |    || ||||  ||  |      ||||||| || ||||| ||||| || ||||||||||| ||||| || |||||||||||  | ||||||||||| |||||||| || || || ||  | |||  
gtatgccatttttttgtgatcgaataaggccatatcgatatttcttttgttgtcatatcttttattta-gactgtctgatttagacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC

upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                     | |  ||    |    |   |   |     ||  | | | |  ||||  ||||||    |  ||| ||      ||| | | |  || | |     | ||||||||||| ||||| || |||||||||||||| || || |||||||| || || ||  | || |||||||| || || || || || || ||| | ||   
-------------------aatttcattagtgtgcaatcactatctctagagatctatagaaatttta--tctgaaca--cggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC

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|125238121|gb|EL252206.1|EL252206
EST:     GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTG                         AGAAGGACTGGGAGGATATTAAATTTGGAGT
genomic: GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattt ... cttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGT
EST: gi|116479876|gb|EG522468.1|EG522468
EST:     GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTG                         AGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTT
genomic: GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattt ... cttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTT
EST: gi|124996516|gb|EL068785.1|EL068785
EST:     AGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTG                         AGAAGGACTGGGA
genomic: AGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattt ... cttgccgcagAGAAGGACTGGGA
EST: gi|86057128|gb|DR352885.1|DR352885
EST:     GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTG                         AGAAGGATTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTT
genomic: GAGACACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattt ... cttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTT
EST: gi|124949637|gb|EL025202.1|EL025202
EST:     CACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTG                         AGAAGGACTGGGAGGATATTAAATTTGGAG
genomic: CACCTGAATGTCCGAGGAAAGAGTGCAACTTTACCTTCAATCACTGgttcgaattt ... cttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
                                      ttattttctt  CT-rich tract
                     atgcttattttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA