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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttcagcgcgattctctctgatctaaatttctgtttcctgtggatgattaaatctggatcggattgtttgattttgaatttgctttttgtttatggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT

Basic information

species Arabidopsis thaliana
transcript AT5G04440.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g05320.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------gtaacttcag---cgcgattctctctgatctaaatttctgtttcctgtggatgatta-aatctggatcggattgtttgattttgaatttgctttttgtttatggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT
                                    ||||  | |   || ||||| |  |   ||     |  ||||   |  ||          ||| | | ||   |  ||| ||    |||||||  | |  ||   || ||  ||||| |||||||| || |||||||||||||||||||| || |||||| | || ||| | || || ||   ||| ||  | || || || ||    ||
gtcggtatctcctagtcctcctcccctcccgagtactaaccccgggctcgggattcgcctttgcctcgcgcttcgtttgtcggagagatccccgccctgaagctgagcctgagatgtt----ttgcttt--gctcgtgtcgtgtagCGGAGTACATGAGCTTGCCGGCGAGTCAGTACTCGGTGCTCGACGCGGAGCGCATCGAGCGCGTCGACGAGTCCACCTTCCGCTGCTACGTCTACCGCTT

upper sequence: AT5G04440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G18400.1 (Glycine max), 3'ss of exon 1
gtaacttcagcgcgattctctctgatctaaatttctgtttcctgtggatgattaaatctggatcggattgtttgattttgaatttgctttttgtttatg-gtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT
   |  |  |  | |   |   | ||  ||  || | |    | |  |   ||  |  ||  |   |     || |    | |||| | |||  | ||| || |||||||||||| ||| | ||||| ||||||||||| |||||| | || ||||||||||||||| | ||  | || ||||||||||| ||||||||||||| |||
---atataggaactaca-tgagtaattaaagcttttctgattt-taaacatttttacttgattttaaaaaactggt---aattttgttgttttatgatgtgtgtgcagTTGAGTACATGCGGTTACCGGCGAGTCAGTATTCGGTGTTGGACGCGGAGAGGATTGAGCGGGTAAACGAAAACACGTTTAGGTGTTATGTTTATAGGTT

upper sequence: AT5G04440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G24290.1 (Glycine max), 3'ss of exon 1
gtaacttcagcgcgattctctctgatctaaatttctgtttcctgtggatgattaaatctggatcggattgtttgattttgaatttgctttttgtttatggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT
 |||   |     || |       |  |||   | |  ||  | |  |   ||  |  ||  |  ||    ||| |  |    |||  |||| |     || |||||||||||| ||| | ||||| ||||||||||| || ||| | ||||| |||||||||||| | ||  | || ||||||||||| ||||| ||||||| |||
ataaaaactaaatgagt-------aattaagccttttcttattttatacatttttacttgattttgaaaaattggtaattttattggattttatgatgtgtgtgcagTTGAGTACATGCGGTTACCAGCGAGTCAGTATTCAGTGTTGGATGCAGAGAGGATTGAGCGGGTAAACGAAAACACGTTTAGGTGTTACGTTTATAGGTT

upper sequence: AT5G04440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g05380.t01 (Vitis vinifera), 3'ss of exon 1
gtaacttcagcgcgattctctctgatctaaatttctgtttcctgtggatgattaaatctggatcggattgtttgattttgaatttgctttttgtttatggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT
               |  | | |||  |  ||   | | |  | || ||| || | | |     | |||  |  ||  || |||| ||| || ||  | | ||||||||||||| ||||| || |||||||| |||||||| ||| | ||||| |||||||||||  | || ||||||||||||||| | |||||||| |||| |||
--------------gtaatgtttgagttgcatggat-tgtattatgtatggttcatttt----tgaatt-ctcaatcgtggatttacttgtt-ttggttggttgcagTTGAGTACATGAGTTTGCCTGCGAGCCAGTACTCTGTGTTGGATGCTGAGAGGATTGAACGTGTGGATGATAACACGTTTCGGTGTTATGTGTATAGGTT

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|116428965|gb|EG471557.1|EG471557
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045783|gb|DR341538.1|DR341538
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         T--AGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045777|gb|DR341532.1|DR341532
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045781|gb|DR341536.1|DR341536
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         T--AGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045778|gb|DR341533.1|DR341533
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         T--AGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045775|gb|DR341530.1|DR341530
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045782|gb|DR341537.1|DR341537
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045780|gb|DR341535.1|DR341535
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
EST: gi|86045776|gb|DR341531.1|DR341531
EST:     CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAA                         TTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA
genomic: CGCTCGTCAGAAACAATCCGTCTCCGTTCGTCAGCTACAGCGACCTCTAAgtaacttcag ... tggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatctggatcggattgtttgattttgaatttgctttttgtttatggtttgcagTTGAGTATATGAGCTTACCTGCGAGTCAGTACTCGGTGCTTGATGCGGAGAGGATTGAGAGAGTTGATGATAACACGTTTAGATGTTATGTTTATACGTT
                 gtttgat  putative branch site (score: 5)
                  tttgattttgaattt  TA-rich tract