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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag----
 ||||| || || ||||| |||||||| |||||||| ||||||||| | ||||| ||| |||||||||||||||||||  |||| || || ||| | || || |||    ||||  | |  |||   |||   ||   |      || |   |||  | |   |||  ||  | | | | ||| ||   |  |||   |     |    
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCACAAGACAAgtaagaa---caaaaacctggtttccctattcctttagc------tcctagattttacatcatatgaatggacgacttcctttattcatgaaatggaaaaaattgatta

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgag---acttccaaacccattctttagata--tgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag
 ||||| || || ||||| ||||| ||||||||||| || || ||||| ||||| ||| |||||||||||||||||||  |||| || || ||  | || || ||   |||| ||      |||| |||  |  | |   |   ||| | | ||   |||  |  |  |||    | |||  ||||    |||   |             
AATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCACCAGACAAgtaagtaaacttgcatgaaatttctgtagccaactatgaaccttatcatatattaactttgtccatcaatggtcaatcaagcacttgaactttgaattga----------

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttt-tgt-tttcgttatgtggactgcag--
 ||||| || || ||||| |||||||| |||||||| || |||||| | ||||| ||| |||||||||||||||||||  |||| || || ||| | || |||||       || |  |||| |    ||       |  |||| |  |    |||   |||  ||| ||  || ||||| | ||  || |  | | |  |   | |  
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCACAAGACAAgtgagc------aatctgttctctgctcatcagggtcatgtcttttgctg---ttctttttttttgtgtgttcatatactgtatgcattccactttctaaatctctgac

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G42110.1 (Glycine max), 5'ss of exon 1
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttca-tgtctgagcaaatacttttgttttcgttatgtggactgcag
 ||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||| |||||||||||||||||||| | || || || || || ||||||| | || || | |  ||    ||| || |  | | |  | | | |||  ||||| || | | ||| | |  ||     ||| || || |||  | |  |    
TATGAATCCAGAAGATGAAGCTGAAGAAGATGGGGCCAACATTGATCTTGACTCTCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCCACTCGACAGgtgacaatttcatatcttttggacagaaatttcatgtcctccctat-ttcgatttccagtgttactgtttcattaagattgtttcttatcttta-atagtgt----

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgtt-ttcgttatgtggactgcag
 || |||||||||||||| || || ||||||||| | || |||||||||||||| ||| |||||||||||||||||||| | || || ||||| || ||||||| |     || |  ||  ||||  || | ||  | | | |  ||    ||||    |   |   |  |   |||| | ||      |      |  ||  || 
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgaca-----aagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca-

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaa-----cccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaat----acttttgttttcgttatgtggactgcag
 ||||| |||||||| || ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||||||| | || || ||||| || ||||||| |    | |      |  ||| | |   | | ||  | |          || ||       | ||| | |    ||       |||   | |   || | | ||||||||
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgt----tttctacatcttctcttccgtttcccgtttcatgtctgagcaaatact--tttgttttcgttatgtggactgcag------------------------------------------------------
 ||||| || ||||| || ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||||||| | || || ||||| || ||||||| |    | |     |  | | |  || |    || ||| ||| |   ||  | ||    | |  |||   ||  | |  |   || |  |  | | | ||||                                                           
AATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggactaggatttcatattgtcatctgatgttcctatatcatagtttaagattgttttatt-tgttatagttattgttatcttatgcttttaacgaggacaagctcttagtacatttttcggtaaccttgagcttaataatgttttcttttgactgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag
 ||||| ||||| ||||| || |||||||||||||||||||||||||||||||| ||  |||| |||||||||||||| |||||||| |||||||| |||||   ||  |   |     || ||| | ||   |  ||| | |  | | |    |   |||   ||    || ||||    || |    |   ||  ||    | 
AATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgt---acaccagcattttctcatta-acatacatg-tacttgtcttttacaaggtagagttaattggagcagtaaatggaattttcgaggacctgcagagcaaaa

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 3
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgag--acttccaaaccca--ttcttt---agatatgttttctacatcttctcttccgttt---cccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag
  | |||||||||||||| ||||| || |||||||| ||| ||||| | ||||| ||| ||| |||||| ||||| || ||||| || || ||||| || || ||  |  |||| |   |  |||| |   ||  | |||||| |||| |     ||  | |        || || ||       |      |  |||  || |||| || |   
CGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttatatccacattgagattctctggcagtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtgtacag---

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|86071052|gb|DR366809.1|DR366809
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGA
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGA
EST: gi|301502331|gb|HO207871.1|HO207871
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071039|gb|DR366796.1|DR366796
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071062|gb|DR366819.1|DR366819
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGT
EST: gi|86071059|gb|DR366816.1|DR366816
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071028|gb|DR366785.1|DR366785
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAG
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAG
EST: gi|86071063|gb|DR366820.1|DR366820
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTG
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTG
EST: gi|86071050|gb|DR366807.1|DR366807
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071057|gb|DR366814.1|DR366814
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTT
EST: gi|86071049|gb|DR366806.1|DR366806
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071047|gb|DR366804.1|DR366804
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071045|gb|DR366802.1|DR366802
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071048|gb|DR366805.1|DR366805
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071065|gb|DR366822.1|DR366822
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCANTTGTTGGACTCGTGGATCCTGATAGTTTG
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTG
EST: gi|86071056|gb|DR366813.1|DR366813
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGGTGGA
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGA
EST: gi|125160706|gb|EL188171.1|EL188171
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTA
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTA
EST: gi|86071038|gb|DR366795.1|DR366795
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGANAGTTTGAAACCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
EST: gi|86071035|gb|DR366792.1|DR366792
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGAT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGAT
EST: gi|86071053|gb|DR366810.1|DR366810
EST:     TCGCAACGGAAAGGAAAAAGGNGTTGGGGTTGAAAACGTCTACACGGCAG                         ACCATCTTTTCTAACCAGTTG
genomic: TCGCAACGGAAAGGAAAATGT-GTTGTG-TTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTT-CTA-CCAGTTG
EST: gi|86071037|gb|DR366794.1|DR366794
EST:     ACTCGCAACGGAAAGGAAAATGNGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGGTGGA
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGA
EST: gi|86071030|gb|DR366787.1|DR366787
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTTCTACCAGTTGTTGGGACTCGTGGATC
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTT-CTACCAGTTGTTGG-ACTCGTGGATC
EST: gi|86071060|gb|DR366817.1|DR366817
EST:     ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCT
genomic: ACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCT
EST: gi|125022321|gb|EL094590.1|EL094590
EST:     CGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAG                         ACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT
genomic: CGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttc ... tggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA