Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG

Basic information

species Arabidopsis thaliana
transcript AT4G38430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
-----gtacattatagtttggagtgtgctttgctggttgcatca------tgaaacgatgcttagataatttaagagtttgtgt-gtgtt-cttg--cagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
      |  | |||   ||    | | || | |       ||||      ||  |  ||  | | |  ||| |    ||| | | ||||| ||||  ||||| || ||||| || || || ||||||||||| |||||  |||||||| |||| || ||||| |  |||||||| ||||||||  ||||||| |||||||
tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G105253_T03 (Zea mays), 3'ss of exon 3
------------------------------------------gtacattatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                                            | |  | | ||   |  ||  ||| ||  ||  || |   ||  ||  | | ||    |  |  | | ||    ||    |||||||| ||||| || || || || |||||||| |||||  |||||||| |||| || ||||| |  || ||||| ||||||||| | |||||||||||||
gtaaagcctgtgcaaagacaagtaaccacctacttattctggccaaaacacaattgataaagtctttttct--ttcaattacacaa--atcataatattcactttgtttctttgaaaatttcc-cagGATGTTGGGCAGTCCATACTTGAAAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATATATGTTGATGATG

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
-----------------gtaca-ttatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                 ||||| |||      ||| |||| || |  |   |   | || |||      ||      |   || ||| | |   |  ||||||||||| || || || ||||| || ||||| || || |||||||||||| ||||||| ||||| | |||||| ||||||||||| || ||||| |||||| 
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttggaacagaaaataagcttctgtggaatttcttt---tcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
----gtacattat-agtttggagtgtgctttgctggttgca-tcatgaaacgatgcttag----ataatttaagagtttgtgtgtgttctt------gcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
    ||   | || ||| |  | | | ||  |  | |||   |   || | ||||  | |    | ||  ||||  | ||||    |||||      ||||||||| || || || ||||| || ||||| || || |||||||||||| ||||||| ||||| | |||||| || |||||||| || ||||| || ||| 
aatggtttgtgattagtgtacaat-tactaagaggattgtggttgggagaagatggctgggaatagaaaataagcttctgtggaatttcttttcgttgcagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtacattatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                 | |  | |   | | |||  |   |||||  |  |||     || |||| | |   |  | |     || | ||  || || |||||||||||||| |||||||| || ||||| || ||||| ||||||||| | || |||||||| | ||| || ||||||||||| |||||||| |||||||
gttagttccattggagaggaattaagcctcttgagaataagttgctt-tgacatagatgaaagatgat-aaccagctcatttacttatctgcattgttacagGATGTAGGGCAGTCAATTCTAGAAAGTTATTCAAGGGTAATGGAGAGCTTAGCTTTCAACATAATGGCAAGGATAGATGATGTTCTTTATGTAGATGATG

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S22_225V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------------gtacattat---agtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaa-gagtttgtgtgtgtt-cttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                                                                                                       ||||| ||   ||  || |||   || |||   ||   |  |    || ||||     |  | |  | ||||  || |  | |  | |||| || || || || ||| |||| ||||||||||| ||| |||||||  |||||||||||||||  ||  | || || || ||  | ||||  |||||  
gtagtcgcatccccgtgtcaattttttgtttgcttgtcatagttgacgtttatttgcatcccaatgttatccttttggaatctgcccgtgatgaactgtaatctacatcatgtgaggctgtagtcgtctctgc-aattcatttttatgtcgttgctattggagctgactgggttttcgtcttctgcacgtagGACGTGGGCCAGTCGATTTTGGAAAGTTACTCTAGAGTGTTGGAGAGTTTGGCCTTCAACATCATTGCACGTATTGACGACGTCGTCTATGCCGATGACA

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 7
-------gtacattatagtttggagtgtgcttt-----gctggttgcatcatga--aacgatgcttagataatttaagagt-ttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
       |  ||||||| ||    || || |       | | ||| ||   ||   | | ||| || |   ||||    |  | || |||     |||||||||| ||||| |||||||| |||||||||||| | ||| |||| ||  | |||||||  ||||   |  | || ||||| || || ||||  ||  || 
tactaatgagcattatacttcatcgtctgttggcataggttagtttcagggtgtttatcaatgtttgggctattttgacgcatcgtttgttgcaatgcagGATGTGGGGCAGTCAATTCTCGAGAGTTACTCTCGAGTGCTGGAAAGTCTAGCCTTCACTATCATTTCGCGTATTGATGACGTCCTGTATGCGGACAATC

upper sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ07173 (Selaginella moellendorffii), 3'ss of exon 5
gtacattatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                 || || | |  |      |||      |||||| |   |     ||           | |  ||||||||||| || ||||| || || || || ||||| || ||| |||||||| || ||||||||||||||||  | || || | ||||||  |||  || || |
-----------------gtatgttctcatatagaaatctc----cgatgcctgacttgcaaaaagaaacaaaactttgtttgcagGATGTTGGTCAATCCATCCTTGAAAGCTACTCCAGAGTGCTGGAGAGCCTGTCCTTCAACATCACGGCTCGCATTGACGGTGTGCTCAATGCCGACGAGG

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|86084700|gb|DR380459.1|DR380459
EST:     ACAAGATTCAGTACAACAAG                         GATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATG
genomic: ACAAGATTCAGTACAACAAGgtacattata ... gttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATG
EST: gi|124717453|gb|EH808855.1|EH808855
EST:     CGGGACTTCCCCAGACAACGCTGGACATGAACAAGATTCAGTACAACAAG                         GATGTAGGGCAATCAATTCTGGAGAGTTACTCTA
genomic: CGGGACTTCCCCAGACAACGCTGGACATGAACAAGATTCAGTACAACAAGgtacattata ... gttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG
                                            tgttctt  CT-rich tract
                    ttagataatttaaga  TA-rich tract