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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctaagatctttagtttcattactcgtttttgatgagattttttttgtatttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG

Basic information

species Arabidopsis thaliana
transcript AT1G54270.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G00950.1 (Glycine max), 3'ss of exon 2
gtaagtcct-----aagatctttagtttcattactcgtttttgatgagat---tttttttgtatttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGG-ATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
|||||| |      |  ||  ||    |  | |   | ||||  | | ||   ||||| |||| ||     ||||     ||   |        | || |  ||  || | || ||||||||||||||||| || ||| |||| ||||||||||||||||| |||||||||||||||||  | |        
gtaagttcctctacagtattcttcacctgttgaaatgcttttattcatatacgtttttctgtaatttgatgtcttgcaaattaactacacagGCTTTCCACTGATGGGCAAGAATTCTTCACCTCATATGACGAAGTCTATGACAGCTTTGATGCCATGGGATTGCAAGAGAATCTTCTGCGAGGCATATAT

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20300.2 (Glycine max), 3'ss of exon 2
gtaagtccta-----agatctttagtttcattactcgtttttgatgagat----tttttttgta--tttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGG-ATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
|||||| |         ||   |   ||  | |   | ||||  | | ||    ||||| ||||  |||| |  ||||     ||   |        | || |  ||  || | || ||||||||||| |||||||| ||  |||| ||||||||||| ||||| |||||||||||||||||  | |        
gtaagttcctctaccgtattcctcacttgttgaaatgcttttattcatataccttttttctgtaaatttgatt-tcttgcaaattaactacacagGCTTTCCACTGATGGGCAAGAATTCTTCACCTCTTATGATGAAGTGTATGACAGCTTTGATGCAATGGGATTGCAAGAGAATCTTCTGCGAGGCATATAT

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------gtaagtcctaagatctttagtttcattactcgtttttgatgag-attttttttgtatttg-ctaatcttattgtttgtt---------tgggtgcagTCTC------GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
                                                   |||  |    |||  ||| |||||||||  | |||| | | |   |||||  ||| |  | ||||| |  ||| || |          ||| ||||| ||       ||||||||||||   || ||||| || |||||||||||  |||| || |||||||| ||||| |||||||||||||| || || |        
gtaagatcttccacttattttttgttttatttttgtttattgttcttcaaagtagttgtgcagaatttt-gtttcattaa-cattttagttaattgtttttcatgtttcagtctaatatgtttgattttgaaaacttgatggctgcagGCTTACATCTGATGGACAGGAT---TTTTTCACATCTTATGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTAT

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------gtaagtcctaagatctttagtttcattactcgtttttgatgagattttttttgtatttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
                                                                              ||  |   | |   |   ||  |  ||| |  | | || | |  |||||  ||   ||     | || ||   | |  |  |    ||| |||||||||||    |||||||| || ||||| |||||  |||| || ||||| || ||||||||||| ||||||||||| ||||        
gtaagattttttatttttattattcggagcaatctggttttattattactgaaattgctgttcgtgttcttgttttgtgttggatatgattgcaacaggat-gttattgctatctgttcaattttttaatggccttatatttttttttccctttcagACTTTCATCT-GATGGACAGGAC---TTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTAC

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 2
---------------------------------------gtaagtcctaagatctttagtttcattactcgttt-ttgatgagatt-ttttttgtatttg---ctaatcttattg--tttgtt-------tgggtgcagTCT------CGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
                                          ||| ||      ||  | |||||||    ||  ||  || |||| |||||  | |||    ||||| |  |||  |||| |       ||| ||||| ||      |||||| ||||||   |||||||| || || ||||||||  |||| || |||||||| ||||| |||||||||||||| || || |        
gtaagatcttccccttattttttgtttattgttcttcaaagtagttctgtaggattctgcttcattagcatttagttactgtgattgtttttcatgtttcagtctaatttgtttgattttgataacttgatggctgcagGCTTACGTCCGATGGTCAGGAT---TTCTTCACATCCTACGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTAT

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------gtaagtcctaagatctttagtttca-----ttactcgtttttgatgagattttttttgtatttgctaatcttattgtttgtttgggtgcag-
                                                   |  ||  | | |  || |  || |      |||   | | | ||  |||  |  || | ||| ||    ||  ||  |   ||  | |||  | || |  ||  |  | || |||||||| || |||||||||||  |||| || |||||| | ||||||||||||||||||||||| || |        
gtaaggaatacactcctcttttttctttccctccctttttttttataatactctgttttgaaaatttcaaatttaaaagtctacctatgtgtaataggatgctaattttcttttcttggttttatgaatcgatgcatacagGCTTTCAACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTAT

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------------------------------------gtaagtcctaagatctttagtttcattactcgtttttgatgagatttttt-ttgtatttgctaatcttattgtttgtttg---ggtgcagTCTCG--ATGGACAGG-ATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG--------
                                                                                 |     | |  |  |||       | |  |        | |  || ||  ||| ||||  |  | || |||  |  |||   || |||| || |  |  ||  |  | || |||||||| ||||||||||||||| |||| || |||||||| ||||| |||||||||||||| || || |        
gtaagttttgttttctatcccttaatcagatggttgttgctgttgcattagcagtaattttccttgtttctttatgttttattgacacaagaacttttgtggatgtgatgctaacgctgtaatgttattaattgaatttcatgttatttttgaataattgatgggagcagACTTGGGACTGATGGACAAGATTTCTTCACATCATATGATGAGGTCTATGAAAGTTTTGATGCAATGGGGTTGCAAGAGAATCTCCTGAGAGGCATTTAT

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|164026466|gb|ES078951.1|ES078951
EST:     CACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATG
genomic: CACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATG
EST: gi|125249475|gb|EL263560.1|EL263560
EST:     AGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
genomic: AGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
EST: gi|125053979|gb|EL124874.1|EL124874
EST:     TTTGACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
genomic: TTTGACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
EST: gi|124818559|gb|EH903425.1|EH903425
EST:     ACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCAATGAGA
genomic: ACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCA-TGAGA
EST: gi|164107226|gb|ES021372.1|ES021372
EST:     GTTTGACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
genomic: GTTTGACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAG
EST: gi|125121092|gb|EL168475.1|EL168475
EST:     GAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAGTTCTTCACCTCA
genomic: GAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCA
EST: gi|124954657|gb|EL029736.1|EL029736
EST:     GAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGT                         TCTCGATGGACAGGATGAG
genomic: GAAGGAACACAATTTGATACGCGTCAGTTTGACCAGAGGCTGAATGAAGTgtaagtccta ... ttgggtgcagTCTCGATGGACAGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgatgagattttttttgtatttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG
                          tgctaat  putative branch site (score: 2)
                                        tttgttt  putative PPT
            attttttttgtatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctaagatctttagtttcattactcgtttttgatgagattttttttgtatttgctaatcttattgtttgtttgggtgcagTCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA