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

TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc...

Basic information

species Arabidopsis thaliana
transcript AT4G28510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 2
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggattttcagta-aatgtattttcccaatgagtttt---tttgctgtttgtgagatttggatgaaattttc
||||||||||| | | ||||| ||| |  ||||  | ||||||||||| ||||| |||||||||||  | ||||||||| | |||||| | ||||||||||||| ||  |  | | | |   | |      |    |||| | |  |||| |  || | || |  ||||   |   || |   |||  | || ||| | |    
TGGTGGGCTTGTTGTATATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAAGATAAGgttattccattgtccatgactgttgaatgaatgatttttttaatgtaatgcaacttgc-aacgccttttgcatcaactttagttgaagtctgtatgtactc---

upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G36940.1 (Glycine max), 5'ss of exon 2
-------TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc--
       ||||||  ||||| | ||||  ||| |  ||||||||||||||||||||||||| || ||||||||  | |||||        | ||| | ||||| ||||||| |   ||       ||||||    | ||| | | || | |  ||     | |   |||| |  |  |  || || |||   | |  | |   ||    
GGATTGTTGGTGGAATTGGTTTGTATGCAGCTGCTAACAGTCTCTACAATGTTGAAGGAGGTCACCGAGCCATTGTTTTCAAC-------TTGGTGTCAAAGACAAGgttattatatgaagaaaaaaattgaaaatgttttgctatttactgcattgcagtgcttgatgactgctact--tggttatgattgtggtgttatgcttgatg

upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 3
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggattttcagtaaat----gtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc
||||||  ||||| | |||| |||| |  ||||||||||||||||||| ||||| || ||||||||  | ||||| ||| |||| ||| | ||||| ||||||| |   ||       ||||||    | ||| | | || | |  ||    ||  |||    |||| || |  || | |   |||  |||    |||      
TGGTGGAATTGGTTTGTATGCTGCTGCTAACAGTCTCTACAATGTTGATGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaattgaaaatgttttgctatttactgcattgcagtgctttggttatga-ttgtggtgttatgcttgatgtttttcagaagag---

upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G01850.1 (Glycine max), 5'ss of exon 1
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtc-agtgtttct-----tcaaattg--ggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc
||||||||||| | | ||||| ||| |  ||||  | ||||||||||| ||||| |||||||||||  | ||||||||| | |||||| | || |||||||||| || | |||   |     | ||||    | | |  ||  ||||    |  |  | ||||  ||     |||  |||  || |||   | |   ||||||     
TGGTGGGCTTGTTGTTTATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAGGATAAGgttattccattgtccatgactgttaaatgaatgatttcctttaatttaacttgcaactctttttgcatcatctttagttgaagtctgt---actcaaatgaaa-----

upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaa---ttgggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc-
||||||  ||||| | ||||  ||| |  ||||||||||||| ||||||||||| || ||||||||  | ||||| ||| |||| ||| | ||||| ||||||| |   ||       |||   |||       || | | || | |  ||     | |   |||| | ||  |   | || |||  ||  |      |||   
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttact--cggttatga--ttgtggcagtctttgtg

upper sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggatt----ttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc
||||||||||||| | ||||| ||||   ||||||| ||||||||||| ||||| ||||| |||||  |||| |||||  |||| ||| | || || ||||||  ||| |    |||    |   |  | |  |   |    | || ||||| ||||||         || | | | | |||| |  |||    | | ||||  
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttc-tcatttccccttggtttcttgcatatgagacctgaaatccattaaat-tatttttgtctctgcttatatggttttttgggtaattgcttttagattt--

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|86047136|gb|DR342891.1|DR342891
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047137|gb|DR342892.1|DR342892
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047139|gb|DR342894.1|DR342894
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047148|gb|DR342903.1|DR342903
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047134|gb|DR342889.1|DR342889
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047147|gb|DR342902.1|DR342902
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047144|gb|DR342899.1|DR342899
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047138|gb|DR342893.1|DR342893
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047143|gb|DR342898.1|DR342898
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047141|gb|DR342896.1|DR342896
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047140|gb|DR342895.1|DR342895
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047152|gb|DR342907.1|DR342907
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047135|gb|DR342890.1|DR342890
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047150|gb|DR342905.1|DR342905
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047145|gb|DR342900.1|DR342900
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACC-TGAGGGTACACACCTTATGATTCCTTGGTTTGAAARGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047149|gb|DR342904.1|DR342904
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
EST: gi|86047151|gb|DR342906.1|DR342906
EST:     GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAG                         GTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC
genomic: GAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagt ... tattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaattgggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa