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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G22425.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 5
gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
   ||   |||  |  |   || |    | |      || || ||  | |    |  |  |  |||||   |      || |   |||  || || ||  |||    || | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| |||
---cttcttttttttttatcatcgatgccatgctatcttttcagtcatgtatactcct--gctatcatcttagaca--gctattgatttattcacttt--gatgaccagCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG

upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
    ||  |||| || | |  |        |   |   | ||||  || |    |  |       || | ||  |   |  ||   |  ||||  | ||    |   || |||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||||||||| |||
-cagtcattttgttcattg--tcaatgcgatgcagccctttctgcattgtaaactcctg------cagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG

upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgt----------ttagtaatcattgaaagtgttgccaa--aaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
                                                     ||||  |   |||    | | | ||   |  |  | |||| |  |  |  ||||          ||     | |||   | | || | ||  ||     |  |  |    |||| |||||||||||||| || ||||| ||  ||||||| || ||||||||||| |||||||| | ||||
gtagtgtatgttgtttaattacttcattaaactttggaattttgctattgagcctctgatgtttccaaatactctttttaatgtgaatcatctatcatgcttcttgttccttttgtctttccctttattcttattattactaatgaaccctctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------gttctctctttgctcctggaattg--tcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
                                                             |||  |   |   |  |  |  ||  || |||||   | || |   | || |   |   ||  |  | |||  |  |  |    ||   || |  |  |    |||| |||||||||||||| || ||||| ||  ||||||| || ||||||||||| |||||||| | ||||
gtagtgtatgctgtttaattacttcattaaagtttagaattttgcctattgagcttctgatgtttccaaatatttttttaatgtgaatcatctttcatgcttgttccttttgtctttccctttattcttatt--atttactaatgaac-ctgctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 5
gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtg--ttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
            |  ||  ||           |    |||  | |   |||| |  |||  | ||| ||  || |    |    ||| |  || |   ||   || | |||||||||||||||||||||||||| |||||||||||||| || ||||| |||||||| || |||
----------gacatctaaaaaaaatcatacctaatcttaggtattggattc-tcatttgtttatccttttaatttatctaatgaaactcattgatttttatcatatttagTTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAG

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|86080767|gb|DR376524.1|DR376524
EST:     GTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAG                         TTGGTGGAGCACTTTTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTT
genomic: GTTACAACTTGGAGATACCAACTCAGAGAGTTGGAACATATGATACTCAGgttctctctt ... cgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG
                                  gtttaac  putative branch site (score: 3)
                                        cctttc  CT-rich tract
                           aaaaattgtttaa  TA-rich tract