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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcttctttccttccatgtgattccagctaatagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA

Basic information

species Arabidopsis thaliana
transcript AT5G63980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
gtaaattgcttctttccttccatgtgattccagctaatagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA
       | || |        ||    | ||   ||   |   || |   || ||     | |      | ||  ||| ||       |||||||| |||||| ||||||| |||||  | ||||||||||||||||| || || ||  || |  |||| || || || || ||||| || ||||| || |
-------gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgt-ttgaatgctg------gcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA

upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
----------------------gtaaattgcttctttccttccatgtgattccag------ctaatagctaactaa----ttttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA
                       |||  |  || |    || ||| |  ||          ||  |||||   | |    | |||  ||  |||||  | |   |   |  | | ||  ||||||||||||||||||||| ||||||||| | ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || || ||||| |
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattact-tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 6
---------------------gtaaattgcttctttccttccatgtgattccagctaat-agctaactaattt--------tcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA
                       | |||  ||| ||  |   || |  ||  || |  | |  || ||  |||        ||  ||  |||||  | |   |   |  | | ||  ||||||||| ||||||||||| ||||||||| | ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || || ||||| |
gtagtactgtttctatagttaacacatt-tttccttattcatatatttttttagtttttcatttagctcttttagatttaatctgcagacatttcttgaccattattact-tcatgaacagAAACTTGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

upper sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 6
gtaaattgcttctttccttccatgtgattccagctaatagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA
                 | |  | |  |    ||  |   || | |  | |  ||     || ||   |     ||| || | |   ||||||||| || |||||||| || |||||  | ||||||||||| || |||||||| ||| |||| ||||||||||| || || ||  | || || |||||||
----------------gtactgtattgtctttgcagacgtcttattgttctctctgtcttatatgcctaa---ttattttctga---acagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTATGGGGCTCTATCCAGAGGAGATGGGGCCATTTATCTTCGCTTCCCTCATA

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|124842465|gb|EH926902.1|EH926902
EST:     CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAAT                         AAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAG
genomic: CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAATgtaaattgct ... taatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAG
EST: gi|116482884|gb|EG525476.1|EG525476
EST:     CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAAT                         AAACTCGGTGTCAAAGCTCCAC
genomic: CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAATgtaaattgct ... taatatacagAAACTCGGTGTCAAAGCTCCAC
EST: gi|125217606|gb|EL231689.1|EL231689
EST:     CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAAT                         AAACTCGGTGTCAAAGCTCCACCAGTCCGTA
genomic: CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAATgtaaattgct ... taatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTA
EST: gi|86080973|gb|DR376730.1|DR376730
EST:     CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCACCATTGCCAAT                         AAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTMT
genomic: CATTCGAAGGAGCTCACTCTCTACATGACTTATCCAGCTCCATTGCCAATgtaaattgct ... taatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA
                                      tatgttgtaatata  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattgcttctttccttccatgtgattccagctaatagctaactaattttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT