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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT

Basic information

species Arabidopsis thaliana
transcript AT5G59420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                               || ||| |  |   | |||| ||   |   || |   |  |  || | |  |  ||  || | | |||| |    ||  |||||||| |||| || |||| ||| | ||| || || ||||||||||||||||| || ||||||||||||||||||||||| |||||    || ||
---------------------------gtaagttttg-caccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttca----gCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                        ||   |  |  |  | | |  | ||| |     |    |   |  |     || | ||    |||   |  ||||||    |||  |||||||| | ||||| |||| ||| |  ||||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| |||||    || ||
----------------------gtaagttttctgcttcccttc--ccttgcacaccattctatgccatatcatggttgcctg-aactgttaatccattttt---cagCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtatt---gacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtga-atttttat-atagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
              ||        |   || ||  |     |||||   |   |   ||  |   || |  | |   |||  |    ||||||| | |  |  | || | |||||||||||||||||| || |||| ||| | ||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| ||||||||||| ||
------------gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
-gtaagtattagtatttacacacaaaaaact-cgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
   |  | || |  ||      |   || || | | |||  ||  ||  |    | | | |||    |  |||      |  |||  || || || |   |    | |||||||||||| ||||| || |||| ||| | ||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| ||||||||||| ||
tccacttgttggagttcttgttcttcaatcttcctgttgcatt--gaagtaactataggcatgc---gtatttattcagtgatgtactt-tatgtaatcatc---acagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
gtaagtattagtatttacaca--caaaaaactcgtattgacttccgactttgtaagatgtatgttaagagt-tttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
     | ||| |  ||   |    ||  |  | | | |   |     ||||||  ||||||  ||  || | |||  |  | || |   | ||  | |   ||     ||||||||||||||||||||| ||||  || | ||||||||| ||||||||||| || ||||| ||||| ||||| ||||||||||  ||||||||||| ||
-----tgttaattcttgttcttctaattacattgaagtatttgttagctttgtg-gatgtactttctgattatttcatactattataact-tatttaatcatt---gcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttata----tagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                          |     |  |  | |   |  ||  | |   ||  |     || |||  |   |  |||| | || | ||| ||  ||     ||||||||||||||||||||| || ||||||| ||||||||||||||||||||| ||||| |||||||| ||||| ||||| ||||  || |||||||| ||
-----------------------gtgagtatattcttgcattaaatatttcagggcatacat-----gtattatctggttaatggtggaactttaatgttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgta---agatgtatgttaagagttttacttttcttgtggttgt-acgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                        | ||  |||  |  ||||       |  || || ||   |    | |||      |  || |  | |  ||   | |  |    ||  |  | | ||   | ||| |  ||   | |||||  | || |||||    || |  ||| | || ||||||||||||||||||||||| |||||||| ||||| |||                 
gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggct-gttttatttcatcatttttcgtgtaagtgcagttcataagcacttcgctgga-gtaataatgaggttcttgtttgtgcagGCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG-----------------

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagt--attagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
 | | |   | ||| | |         |   | |||  ||  | |   |||  |||  ||       |     |||| |||||    |  |  ||    |  | |  |||  |||||||  |||| || ||||  || |     || || ||||||||||||||||| ||||| || ||||| |||||||||||| || |   |||  |
atcacttcgtcagtgtatctcttgcttatgtttgtaaggaagtaccgttttacaagcagt-------ggcggctactgttcttacactatt--gtcgcctcatttgcagCTACATGGGCAGTATCGGTGTACTTCGCATATGCGCGGACCTGGAAGCCTTTCAATCCCATTCTCGGTGAGACCTATGAGATGGTCGACAAGAATGGCCT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacg---tgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                                                        ||| ||   || || |  || |   ||| |  | ||   ||  || || || ||| |  |||||||| ||||| || ||||| | | ||||  | |||||||| |||||||||||||| |||||||| ||||| ||||| || ||| |||| ||
--------------------------------------------------------gtaagtggtgaattctctttctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAACGTGCGTGGAAGCCATTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttg------tggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                                                 |||||  ||   ||     | || ||   | ||      || ||     ||  || || || ||| |  |||||||| ||||| || ||||| | | | ||  | ||||||||||||||||||||||| |||||||| ||||| ||||| || ||| |||| ||
-------------------------------------------------gtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT

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|47827935|gb|CK117619.1|CK117619
EST:     GGATCAAGCAGATGAATGCGAAGATCCATACTTGCGTTTAGTATATGCTT                         CATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTT
genomic: GGATCAAGCAGATGAATGCGAAGATCCATACTTGCGTTTAGTATATGCTTgtaagtatta ... ttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
                                            tttttat  CT-rich tract
                                        tgaatttttatata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG