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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata...

Basic information

species Arabidopsis thaliana
transcript AT4G09800.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttg---agcttttgttgctctt-ctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata----------------------------------------------------------------
| ||||||||||| ||||| || |||||||| |||||||||||||| ||||||||  ||||||||  |||||||||||||||||| |||||||||||||||||||     ||||  ||||  ||  |    || || || ||   |   ||  |   |  |||||  |||  |||   | | |   | |   | |||   | |                                                                 
GGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAGGTATTGGGAGGCGATTTTCTAACATTTGCTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcag

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G08690.1 (Glycine max), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagtt-ttgagata
| ||||||||||| ||||| || || |||||||||||||||||||| |||||||| |||||||||  |||||| || |||||||||||||||||||| ||||| |   |  ||   |  || |   | | |  ||||||| |||    | |  | | |  |  |  |   | | | |     |||  |   | ||   | |
GGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAGGTATTGGCAGGCGATTCGCTAACATTTGCTGCAAAAAAGCTGATGTCGACATGAACAAGAGgttcggtttcatgaaacctttgtttttgttttattctttattgtcggat-agttaagtctttgccatgaggttgtgtcatttagttttttctattcttaca

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G36610.3 (Glycine max), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttg-tctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata
| ||||||||||| ||||| ||  | ||||| ||||| |||||||| ||| |||| || ||||| |  ||||||||||||||||| ||||||||||||||||      |||| ||| |    | |  ||| || ||  || |       ||      |||||   | ||| ||| | |||      |              
GGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGGGTATTGGAAGGAGATTCGCCAACATCGCTTGCAAGAAGGCTGATGTTGACATGAACAAAAGgtgcttttttttattggttgagttcaattgctcgttaattcgcacatttttgtggttattgttgaaattgggattt-ttgtttgtcag-------------

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G24710.1 (Glycine max), 5'ss of exon 1
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtctttctttagtgtgaacttaaatcaat-tgtgacatttgagatatattgaagagtaatagttttgagata------
     |||||||| |||||||| || |||||||||||||||||||| |||| |||  ||||||||  | |||| |  ||| |||| ||||||||||| |||||||   |  ||   |  || |   | |  |    ||  | |||     | || | |  |      |     ||| || || | |||   ||||  || |      
-----CAGAAGATAATGTTTGCTCTCACCTCTATCAAAGGTATTGGCAGGCAATTCACTAACATTTGCAGCAAAATAGCTAATGTTGACATGAACAAGAGGTTTGgtttcatgaaacctttgtttttgttacagggttgggggtgg-tacacattagtgcgcagtcatgtcattatgttcaaaa-taaaccttttttgacagtgtag

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G30970.1 (Glycine max), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtct-----ttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata
| ||||||||||| ||||| ||  | ||||| ||||| |||||||| ||| |||| || ||||| |  ||||||||||| ||||| |||||||||||||||| |    ||       | |  |  |||    |     ||  || |  ||   ||      |||||   | ||| |   | |||     |  |  || | ||   
GGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGGGTATTGGAAGGAGATTCGCCAACATCGCTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtgtttttttaaaaaaatttgttgagttcaattgcacgttgattcgcatgtttttgtggttattgttgaaattgggtgtttttgtttgtttgt--ttgtcag---

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacg---tttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata
| || |||||||| ||||||||||| || || ||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||||||||||| |  || |||  |  | ||||| |   | ||| |   || |  |  ||  |     ||  |    |||||  || | | |   |   |    ||   | ||
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatggg--aaaggaaggatttggaattt-tagttaatgcacttcttaatgcta

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ25542 (Selaginella moellendorffii), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata
|   ||||||||||||||| || || || || ||||| || |||||  | ||||| || ||||| |||||||||||||| ||||| ||||||||||| |||| |    |    || || |||  | |       |  | ||    ||  |       |   | |||||     || ||   |  |     | |   ||| 
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtattgtttgccctttcttttcctcttgctctgctggtgagctgaaagatcttgttttctcgtcattttcttgatctttcgggttgggcttctatggatg

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 2
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgt----ttgagcttt-------tgttgctcttcta----------------cgttt----gtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaa-gag-----taatagttttgagata---------------------------------------------------
|   ||||||||||||||| || || || || ||||| || |||||  | ||||| || ||||| |||||||||||||| ||||| ||||||||||| ||||    |||  ||||       | ||||||| ||                  ||||    ||| || | |  | || |     |||     |||  |||  |||  |||||  |||     | || | ||||| | |                                                   
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtatgtttgccctttcttttcctcttgctctgctggtgagctgaaagatcttgttttctcgtcattttcttctatggatgactatcttccttgatctttcggattgattgattgagcttcttcattgatttgaaaaaaaaaatctgtgcttatcatttttctttgtttctttctcttccatcgaacag

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|164153103|gb|EL993293.1|EL993293
EST:     GAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: GAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|125264893|gb|EL278978.1|EL278978
EST:     CTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|86077988|gb|DR373745.1|DR373745
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|116431165|gb|EG473757.1|EG473757
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|164078765|gb|ES133277.1|ES133277
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGC
EST: gi|164184060|gb|ES091101.1|ES091101
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGAACTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGG--CTGGTGAGTTATCTGC
EST: gi|86081140|gb|DR376897.1|DR376897
EST:     ACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: ACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|125049263|gb|EL121532.1|EL121532
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTG
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTG
EST: gi|164029431|gb|ES175245.1|ES175245
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGTAGGCGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagcttttgttgctcttctacgtttgtctttctttagtgtgaacttaaatcaattgtgacatttgagatatattgaagagtaatagttttgagata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagagtaa