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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcgggcattgatgattatcattgtggctcttcttcag

Basic information

species Arabidopsis thaliana
transcript AT5G48760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G46850.1 (Glycine max), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcgggcattgatgattatcattgtggctcttcttcag
| ||||| || |  |||||  | ||||| |||||||| || || ||  ||||| |||| |||||||||| ||||||||||||  ||||||||||||||||||  |||    ||     ||||||| ||    ||||| ||   ||    |||| |  |     ||| | |  | | ||    |  |      
CAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTCCCTGATGCTCTCAAgtgagttttactttgtgcttttgtt-ttggaatttggttcttcaa----tctattatgaatgctgaag-tggtgaatgaaatttattag---

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G46860.1 (Glycine max), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcgggcattgatgattatcattgtggctcttcttcag
| ||||| || |  |||||  | || ||  ||||||| ||||| ||  ||||| |||| |||||||||| ||||||||||||  | ||||||||||||||||  |||  | || | | ||||||| ||    ||||| |    ||   ||    | | |   | |   || |   || |             
CAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagtttttctttctacttttgtt-ttggaatttggttgttcaatcttttagatgctgaagtggtgaatgaaatttattag----------

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G13670.1 (Glycine max), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcg---ggcattgatgattatcattgtggctcttcttcag-------
| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| |||||  | ||||||||||||||||  |   ||||| | | | || || |   ||  |  ||       |  | || || |   ||| |  |  |  | | |  | |   |  ||||        
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCTCTCAAgtaaga--ctttttctactgtttttttatgctaatatatttaattttaatatagtttgataggcctacactagcaacctatttgaaatcattcattgtacat

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G02790.1 (Glycine max), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttg--ttcttctcttttggatccgt---aactgttctactt-cgggcattgatgatta-tcattgtggctcttcttcag-
| |||||||| |  |||||  | || ||| ||||||| ||||||||  | ||| ||||||||||||||| |||||| |||||  | |||||||| |||||||  |    |||     ||| ||  |  ||   ||||  ||  ||   ||  |||  |    |  | |||   ||  | |||     | | ||  | |  
CAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTTGTTCCTGATGCACTCAAgtaagagtttttctgtctttctgaatcgtttagttttcaatatgtgtcaagagtttaataagcacgtattagcgacaaatcagaaatgatgttgataaat

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccattt--ttgttcttctcttttggatccgtaactg---ttctacttcgggcat-tgatgattatcattgtggctcttcttcag-------------------------------------------
| ||||||||||| || ||  | |||||  ||||||  ||||| ||  | ||| | |||||||| ||||| |||||||||||||| |||||||| |||||||| ||| ||| |  |  ||  || |  || ||| |    | | ||| ||   ||    |||  |  | |  |  || | ||  ||  | ||  ||                                             
CCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattag

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 5'ss of exon 2
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaact-gttctac-----ttcgggcattgatgattatcattgtggctcttcttcag--------
| ||||||||||| || ||  | ||  |  ||||||  || || ||  ||||  |||||||||| ||||| ||||||||||| || ||||| ||||||||||  ||||  | |   | |||| || ||   ||||   |   ||  | |  |||       | |    ||   || | | ||  | |   || ||  |        
CTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTTATTCCTGACGCTCTCAAgtgagttctgtatttgagttttattttttattttttattttttatttaggcctataaattcttgttggtttgagactttaatgcttgagatttttgggaaaatcag

upper sequence: AT5G48760.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S174_48V6.1 (Physcomitrella patens), 5'ss of exon 3
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgtt--ccttttaccatt-tttgttcttc-----tcttttggatcc--gtaactgttctacttcgggcattgatg---attatcattgtggctcttcttcag---------------------------------------------------
| ||| | |||||||||||  | |  ||  |||||| ||  || ||||| ||  |||| || ||||| || |||||||||||||| |||||||||||||||| || |  | || |  || | | || | |       |  ||   ||    || ||   | |  |||| | |   |||     | |   ||  |   |  || ||                                                   
CAAAGAGGGGAGCTGCTGCTCTTGAGCGCTTGAAGGCATTCGAGGGTGTCCCAGCTCCTTACGACAAAATGAAGAGGATGGTCATTCCTGATGCTCTCAAgtatgctaactttctcgcactgtctgatgtcaagaagtgattataatttaggttaccagtatgattcgaggaccaatgtaggctgttgctgcagaattgttttagactaataaatcaatgttattgtgtcgttcatgagacgttttatttatgcag

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|86017893|gb|DR313639.1|DR313639
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTGTTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|164237574|gb|ES093914.1|ES093914
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTC
EST: gi|125039186|gb|EL111455.1|EL111455
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTT
EST: gi|86017891|gb|DR313637.1|DR313637
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTGTTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|86017890|gb|DR313636.1|DR313636
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGT
EST: gi|86023702|gb|DR319455.1|DR319455
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCT
EST: gi|86017895|gb|DR313641.1|DR313641
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTGTTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|47831264|gb|CK120948.1|CK120948
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|86023706|gb|DR319459.1|DR319459
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|125264433|gb|EL278518.1|EL278518
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAA
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAA
EST: gi|47827976|gb|CK117660.1|CK117660
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|86023705|gb|DR319458.1|DR319458
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGC-GTCT
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCT
EST: gi|86017892|gb|DR313638.1|DR313638
EST:     CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTGTTGGGCCGTCTTTC
genomic: CCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
EST: gi|164220530|gb|ES042158.1|ES042158
EST:     CCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC
genomic: CCCTGATGCTCTCAAgtttgttcct ... tcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCATCCCTGATGCTCTCAAgtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcgggcattgatgattatcattgtggctcttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG