Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG

Basic information

species Arabidopsis thaliana
transcript AT5G19990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 2
------------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                         | | |  | ||||| | ||     |  ||  | |  |   |    ||  | |||    | || |   ||| | ||||| |||||||| || || ||||| || |||||||| ||||| || || ||||| || ||||| || ||||| |||||||||||||| |||||||||||| 
gatctgtcacattgtcatttggttctgttagccctttttgtaatggaaatcctaaatttctgtttaccagtgctattaacttct-caatataattattcagGTACATCCAGAAGGCAAATATGTGGTGGATATTGATAAAAGCATTGATATTACAAAGATCACACCTTCAACAAGAGTTGCTCTTCGAAATGATAGCTATA

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
------------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                        |     |  |||||  | ||  | |      ||     ||  |   |||    |  | | | | | | || || ||||| || ||||| || || |||||||||||| | || |||||||| || ||||| ||  || | || ||||| |||||||||||||| ||||| |||||| 
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaacatttggtaaatctttctgtgttaattgatca-attgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 2
-----------gtat-gaatcttttttattatcatgttt----gtatttctacgaacatagttgtcagtaaggcttacactccc-------attttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
            ||| | |    || | | | |||  |     | | |||||    | | |||||||    |   |  |||  |       |||   ||||| || || || || || |||||||||||||| || || || || || || || || ||||| || ||||| ||||| ||||||||||||||||||||| 
aaatattgttattattggactgcttatctgagcattctcaatgggagttctaacttcctggttgtcaaagtgatatcaactttctaatgaaattgctcagGTACACCCCGAAGGCAAATATGTTGTTGATATAGATAAGAGCATTGATATCACAAAGATCACACCTTCAACAAGAGTCGCTCTTCGTAATGATAGCTATA

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 2
-----------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                         |    || |  | ||||  |     | ||    || || ||   |     | |   || |  | |  || | ||||| || ||||| || || ||||| |||||||||||||||||||| |||||||| || || |||||||| || |||||||| ||||| || || || ||||
ttatgcaatgtttagttctgaaaacacacgtcatcctaattaataaaacaggatcaaaaccaagatcaattgtgctgatttttcctttactcttcttcagGTCCACCCAGAAGGAAAATATGTCGTTGATATTGACAAAAGTATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTTCGCAACGACAGTTATG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
-----------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                         |   |||| |   ||||  |    || ||     | || ||   |     | |   || |  | |  || | ||||| || ||||| || || ||||||||||| |||||||||| ||| |||||||| || || |||||||| || |||||||| || || || || || ||||
ttatgcaatgtttagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtatgaatcttttttattatcatgtt-tgtatttc-tacgaacatagttg--tcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                    || |  |   ||| |  ||  |||  |||||    |  ||    || ||  |  |       ||   |||   |||  ||||||||||||| ||||||||||||||||||||||| || |  |||||||| || || ||||| || |||||  ||||||||||||| ||||| |||||||
atttctctaccattttcttttacggctgaatttaacaatgttgtgatgtatgaaatgtgagttcagatgatttggctgataatattttccttctttttagGTTCATCCAGAAGGGAAGTATGTTGTTGATATTGATAAGAACATAGACATCACTAAGATCACACCTTCAACCCGAGTTGCTCTTCGCAATGACAGCTATG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtatgaatcttttttattatca-tgtttgtatttctacgaacatagttgtcagtaa--ggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                     | |  | |    |    | || ||| ||  |||||     |||   | |   ||     |||    |||   | | ||||| |||||||| |||||||||||||| ||||||||||| |  ||||| || || || ||||| |||||||| ||||||||| | || |||||||||||||
gttgtctgtgtgggtacattttgtagaacccgatagcaaacagtgtatggttttcttgtctcatttctatggttattcaccttcttttccttgtgttcagGTACATCCAGAAGGGAAGTATGTTGTAGATATTGACAAGAACATAGATATCACAAAGATCACACCATCAACTAGAGTTGCTTTACGGAATGATAGCTATG

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|86057914|gb|DR353671.1|DR353671
EST:     ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
genomic: ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
EST: gi|124748480|gb|EH838610.1|EH838610
EST:     AAAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
genomic: AAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
EST: gi|124751952|gb|EH842082.1|EH842082
EST:     GAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
genomic: GAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
EST: gi|301502412|gb|HO207952.1|HO207952
EST:     ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
genomic: ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATT
EST: gi|125107924|gb|EL161051.1|EL161051
EST:     ATGTGGGAGAAGTGGTAAAAGTTATGGG-AAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTA
genomic: ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTA
EST: gi|125182837|gb|EL198056.1|EL198056
EST:     ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAG                         GTTCATCCAGAGGGGAAG
genomic: ATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAGgtatgaatct ... cattttccagGTTCATCCAGAGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG
                                 ggcttac  putative branch site (score: 3)
                                       cactcccattttcc  CT-rich tract
      tatttcta  TA-rich tract