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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
                   |  |||   |  |||| ||    |  ||     |      | | ||   ||  || | |     |  | | ||||||||||| |||  ||| |||||||| |||||||| |||||||| |||| ||| |||||||| |||||||| || ||| | ||  | || ||||| || ||
-------------------gtaaattggaagatcaatacacctcattcagacactaacagatgattt-ttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 3'ss of exon 2
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgcca---ttgtctg-gcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
||  |  ||      || | |      | || |   | |||  |  |||      || || | | || |    | | || |     || |||| ||||||||||||||    || ||||||||||||||||||||||| ||  ||| |||||| ||||| | ||||||||||||| | ||  | || ||||| || ||
gtgaggatcgatgcacacaccacgctgctgatttcgttttttcttctttttttttttctgttcaggcatgtgcgaagttactctgcttctctgtgcagGTATCCAGACGTCAGAGGACTACAGATTCTACGCCATTTCGGCCAAGTACCCTGAGTTCAGCAGCAAGGACAAGACCCTCGTGCTGCAGTTCTCGGTGAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgt--gctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
                   | ||||   | |      |   || ||  |   || || |  | |||| ||||             |  | | |||||||| || |||   || |||||||| ||||| |||||||||||||| | |||||||||||| |||||||| |||||| | ||  | || ||||| || ||
-------------------gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgtt-------------tcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 2
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
         |   | || | |  |||| |  ||   |  ||   ||||             | ||| |||  | |||      |  | | |||||||| || |||   || || ||||| ||||| ||||||||||| || | |||||| ||||| |||||||| |||||| | ||  | || ||||| || ||
-------gtaaattccaaaac--atcagaagattggtggtttcagttt-----------atttatgagttact-caacacgtttcttgttgcagGTATTCAAACCTCCGAGGATTACAGGTTCTATGCCATTTCAGCCGAATACCCTGAGTTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 2
------------gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttg-tgctaa------tgcgttgttg--caattgccattgtctg-gcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
            |    ||| | |  ||     | ||  |    ||||  |||||| ||    ||  ||| |  |||      |  ||| |||    | ||    | |||  |||||||| || |||||||| || |||||||||||||| ||||||||| ||| |||||||||||| |||||||| |||||  ||||||||||||| || |||||
gtaaactaaattgctatattgaacagtcttgtattatttcttgctcat-gtttatttttggctaaaattgatattaagatatgtttgtttttggctgaatgttgatatctatgcagGTATTCAAACCAGTGAGGATTACAGATTCTACGCTATTTCAGCTCAGTACCCTGAATTCAGCAACAAGGATAAGACACTAGTCTTCCAATTTTCTGTCAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 2
--------------------gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttg--caattgccattgtctg-gcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
                    | ||  |   |  ||      | ||    |  ||||  ||  || | ||  ||  |  |  |||    |  |||    | ||    | |||  |||||||| || |||||||| || ||||||||||| || ||||||||||||| |||||||||||| |||||||  |||||  ||||||| ||||| || || ||
gtaaactaaattgctatgttgaatagtcgggtattatactattattgttgc-tcatgtttacttttgtttaaaattgatattaagatatgtttggttgaatgttgatatctctgcagGTATTCAAACCAGTGAGGATTACAGATTCTATGCTATTTCAGCTGAGTACCCTGAATTCAGCAACAAGGGTAAGACACTAGTCTTTCAATTTTCTGTTAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctgg---------cagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
                                               ||    |    |||   |      |   ||  |  | ||||   || | |    | |     |  |  ||    | | |   || || ||          ||||||| ||||| ||||||||||| |  ||||| || || |||||||||||||||||||||||||||||||| ||||| || || ||||| || || || ||
gtatgctatccatcattatactgtctgtacattaacaaagacgaaaagtgctttgagacctcttgcttctgtttaagggttctcatttcaggtgtgattttccttattaagagttttcagactacttatatggtttgaatctgggtccagGTATTCAGACTAGTGAAGACTATAAGTTCTATGCAATCTCAGCTGAGTTCCCTGAATTCAGTAACAAGGATAAGACTTTGGTTTTCCAGTTTTCTGTTAA

upper sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 2
------gtatgattcagccttcagagctaatcacagaatcattatttattgt-tttacaagcttgtgct----aatgcgt----tgttgcaattgccattgtctgg---cagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
       | | || ||   |      |  ||    |    ||  || ||| | ||||  |  |||  ||    |||| ||    || |   | | | || ||||||    ||||||||| || ||||| |||||||||||||| || || |||||||||| |||||||||||| ||||| || ||||| ||||| ||||||||  | || ||
gtattattttcatacacattcttatacctatt-tggggcaatgtttcattctctttattaatttggactttgaaatgtgtaacttgatttgacttcaatggtctggatatagGTATCCAAACAAGTGAGGACTACAGATTCTATGCTATATCAGCTGAGTACCCTGAATTCAGCAACAAAGATAAGACATTAGTTTTCCAATTTACTGTTAA

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|309381116|gb|HO850337.1|HO850337
EST:     GGAGTGGAAGCACACTGCGGGAAATTGGTCTGGTGACGCTAACGATAAAG                         GTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCC
genomic: GGAGTGGAAGCACACTGCGGGAAATTGGTCTGGTGACGCTAACGATAAAGgtatgattca ... tgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA
                   tgctaat  putative branch site (score: 2)
      ttttacaa  TA-rich tract