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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata...

Basic information

species Arabidopsis thaliana
transcript AT5G27720.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta--atttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata--
|| || ||||  |||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| |||||||||    |||||    |||       | | ||     ||||||   | ||||  |  ||||     |     || | || |     |  ||  ||||||     
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaaccttgtttactatgtgcttg---tggtttgctggttgtatgtttagacatgta-tgttctccatctgcataatcagccttt

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G095114_T01 (Zea mays), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgt---aatttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata
|| || || |  |||||||||||||| || ||||| || ||||| ||||| || ||||| ||||||||||| ||||||||   ||||| ||  |   || | ||   || |     |    | | |  ||  || ||| | | | |||           | ||  ||  ||   |||    
GATGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGTGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatgaatttcttggttaatgagggtagctacactctatttcagttttgcttggttgtttatgcgcttctaggcttctactttatttttttccttgtcat---

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G038606_T03 (Zea mays), 5'ss of exon 3
----------------------GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta-atttttttttgtgtgtgtgtgtatata-tctcttgcttgatctagtttt-ttctttgttcccctctctctggaatgatgatgcttagccaaatcagata
                      ||||| || |  |||||||||||||| || ||||| || || || ||||| || ||||| ||||||||||| |||||||||    ||| || ||   || |  ||   | |||||   |   | | | ||  || ||| |   | |||| |||   |  |    |||  |   || | || 
TTTATGATGGCTCGAATTGCAGGACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatggatttcttggttaatgagcctagccaatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttc---cttgtcattatgacatg

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G038606_T02 (Zea mays), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta-atttttttttgtgtgtgtgtgtatata-tctcttgcttgatctagtttt-ttctttgttcccctctctctggaatgatgatgcttagccaaatcagata
||||| || |  |||||||||||||| || ||||| || || || ||||| || ||||| ||||||||||| |||||||||    ||| || ||   || |  ||   | |||||   |   | | | ||  || ||| |   | |||| |||   |  |    |||  |   || | || 
GACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatggatttcttggttaatgagcctagccaatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttc---cttgtcattatgacatg

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G39780.1 (Glycine max), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgctt-agccaaatca-gata-
|||||||||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| ||||||||   | | || ||||||   |||   ||  |  ||  ||  | || || ||  |||     | | |   |||  |||  |      | ||    || | || 
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTATATACGAGGCAATACAATCAAGTACCTTCGAGTTCCTGATGAGgtg--tgtattgtgtgtgca-gtgctaatgacattttatttttttatttgttaatttaaaaacttgtaaatgggttgagaagaagggaaccttgccacggtag

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G37170.2 (Glycine max), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttttttgtg-tgtgtgtgtatatatctcttgcttgatct---agttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata
|||||||||||||||||||||||||| ||||| || || || || || |||||||||||||||||||| || ||||||||   | || | |||| ||||   ||     | ||||  || || |   | ||||     || |    |   |  | |   | |  || | |||| |  |    
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTACATACGAGGCAATACAATCAAGTACCTTCGAGTACCTGATGAGgtgtgtattgtgtgtggtgtgctggtgacattttctttttttatttgttaattttaaaactggtaaatttgttgagaagaaagggagccttgccacagta----

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G17430.2 (Glycine max), 5'ss of exon 4
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaattttt-----ttttgtgtgtgtgtgtatatatctcttgcttgatctagttt----tttctt------tgttcccctctctctggaatgatgatgcttagcca---aatcagata------------------
|| ||||||||||||||| | ||||| || || || || ||||| || || || ||||||||||| ||||| ||||||||   |  |     ||  || | | ||| | |   ||| |   |  ||   |||      |||||      |||      ||||| |  |||       ||| |||   | | | ||                   
GATGGAGATAGATTTTGGCGTATGCCTGAGTGCTACATTCGTGGCAATACCATTAAGTACCTTCGGGTTCCTGATGAGgtgtgtgctgctgcttcagtatttttgttttttgctctttcagtgaataaggttcagaacttcttagggaatgtcgtaagctctcggtgatgcatgcatttatccactgatttaaatttacttcctgttcatttag

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta-atttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata
|| |||||||| |||||||| ||||| || || || |||||||| || ||||| || || ||||||||||| |||||||||  | |    |  |       ||| ||       |   ||| ||     |   ||  |    |  ||| ||    | ||    || | |  ||    | 
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt-

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|86050911|gb|DR346666.1|DR346666
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGG
EST: gi|124753869|gb|EH843999.1|EH843999
EST:     AATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|86050917|gb|DR346672.1|DR346672
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGATAGAA
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGATAGAA
EST: gi|164083471|gb|ES106370.1|ES106370
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGATA
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAGATA
EST: gi|47831834|gb|CK121518.1|CK121518
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|47832106|gb|CK121790.1|CK121790
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|116449433|gb|EG492025.1|EG492025
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|86050907|gb|DR346662.1|DR346662
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAMGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|86050915|gb|DR346670.1|DR346670
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|164215831|gb|ES026114.1|ES026114
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAA
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAA
EST: gi|124748097|gb|EH838227.1|EH838227
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACG
EST: gi|86080718|gb|DR376475.1|DR376475
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|86050918|gb|DR346673.1|DR346673
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGAC-CGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|116480858|gb|EG523450.1|EG523450
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|86050914|gb|DR346669.1|DR346669
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
EST: gi|116480849|gb|EG523441.1|EG523441
EST:     AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAG                         GTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG
genomic: AATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttt ... ctctcttcagGTGATTGATAAAGTACAGGAGGAGAAGACACGCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgtaatttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaga