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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag

Basic information

species Arabidopsis thaliana
transcript AT3G49010.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagta--gtagtaatgtcaacacttctga---tattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag
|||||||| |||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | ||    ||  |  | |||||| ||     | |       | | |   |||   | ||  ||  |  |  |   | |  |          | | ||  |   ||   ||||| |  | |    
CACAACAACGTTATCCCCAATGGCCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATTGgtgagctccctggcctccctatcgcgcatgactatgttagcaattgccactagtactgcatgtgcttgaatttatgaattaaatacggttatctccttct---

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgtta-gtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtctt---attatgttatgttgtacacag
|||||||| || ||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | ||    ||  |  | || ||| | ||  | |   | |    |  | |   ||  | ||||       | ||   |   ||   ||    | | || |   ||| || | |||   | |   
CACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtaaagtgattgatctcttgcgatctatctaatgattatgtgaatgaatgagc--atgttagcttcctacttgctcgtgagattgtgctgtgtaacatatgc

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattgtca---tgtttcgt-tttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag
|||||||| ||||||||||| || |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | ||    ||  |  | || ||||||   |  |    | | |   | | |   |  ||   |||| |||  || | || |      | |   ||   |   || | ||  |||   | || | 
CACAACAACGTTATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgttagctcttctgtgcttaccctctttcagccttccaatatgttgcgtgcttgaattcaagacttagttgtttacaga--tagtttgccatgccctgcaaat

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G145280_T01 (Zea mays), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgt-tagtagtagtaat--gtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatc--tctttgggtcttattatgttatgttgtacacag
|||||||| || |||||||| || |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | ||    ||  |  | || |||    |    |      |||  | |||      |    |   |   ||  | | ||  | | |||    | |||||   ||    |  ||    |  ||   
CACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtacgctcaccgccgcccgtccgctctttcagcctacctactatattttgcatgcttgaattccaactagtgtttggcaattggc-taataaacagctcat--

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G081102_T03 (Zea mays), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagt--agtagtaatgtcaacacttctgatattgtcatgt-ttcgttttaagtttacacta--caatctctttgggtcttattatgttatgttgtacacag
|||||||| || |||||||| || |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | ||    ||  |  | || ||| ||   |     | | |  |  || |  | |   |   |  | | | || | || | ||||   |||      |   ||| |  ||     ||| |     
CACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAGCAGAGGCGCCGCATCGgtgagctcatcgccattttttagcctacctacaacatttcgcgtgcttgttgaattcaaactagctaataaacaggtcacttgtcctgcc-cattgcaatt--

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G14640.2 (Glycine max), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtca-acacttctgata----ttgtcatgtttcgttttaagtttacactacaa-----tctctttgggtct-tattatg-ttatgttgtacacag--------------------------
|| |||||||||||||||||||| ||||||   |||||||||||||| ||||| ||||| |||||||| ||||| ||  |||| || |||||| |  | ||| | |     || | ||     ||| ||| |    ||   |  ||  || |||   ||       ||     ||   ||| ||   ||||||| |||  ||  |  |                            
CATAACAATGTTATCCCCAATGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACCTGGTTCAATCAGCCAGCACGGAAGACAAGAAGACGGTTGGgtaatttaacatattttcttgttcttttgaaacttcttagtaatttctgtgttagtcttttgtggtaaaaagatcagcttgagttagtattatggttacttttaattctttgacatgttattgctgtattcttcag

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G34760.3 (Glycine max), 5'ss of exon 3
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtag----------tagtaatgtcaacacttctga--tattgtcatgttt-cgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag----------------------------------
|| |||||||||||||| || || ||||||   |||||||||||||| ||||| ||||| |||||||| ||||| ||  |||| || || ||| || | ||| | |            | || || |  | |||| | |   |||  | ||||    ||||  ||| | |  |  | |   |||  |  || |||     ||||     |                                   
CATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCACGGAAGACAAGGAGACGATTGGgtaatttaacatattttcttgttattttgaaactttttagtaattaccgtgttagtcttttgtgttaaaaagatcaacagattgaat--tagtattgatggttgcttttaattctttgaaatgttgctgttgctgtattcttcag

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G08090.1 (Glycine max), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaa-------------tgtcaacacttctgatattgtcatgt------ttcgttttaagt--ttacactacaatctctttgggtcttattatgttatgttgtacacag-----------------
|| ||||| |||||||||||||| |||||||  || |||||||| || ||||| ||||| ||||| || || || ||  |||| ||||||||  |  | ||| | |  ||  ||             ||| |||| |  || |||  | |  |      |  ||||| | |  ||    | |||      ||  ||   ||  ||||| ||| |||| |                 
CATAACAACGTTATCCCCAATGGGCACTTCAGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCACGGAAGACCAGAAGGCGTTTAGgtaatttttaccaaaattattgctctttgttaacattgttgctataattaattaatcaatcagtttttaatacttgttatgcaagaaaagtgaatcaacttgagttattttg-acacgggggtgacacattttcag

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 5'ss of exon 1
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattgtcatgtttcgtt-ttaagttt--acactacaatctctttgggtcttattatgttatgttgtacacag-
|| ||||||||| | || ||||| |||||||| |||||||||||||| ||||||||||| ||||||||||| |||||| | |||||| |||||||| |||||   | |   |  | ||  |     | |  |   ||| | | ||  || |||||  | || |   |   ||||  |    |     ||   | |       
CATAACAATGTTGTGCCTAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACTTGGTTCAACCAACCTGCCCGCAAAACCCGAAGAAGAGTTGgt--atgggctttttctcttctaggttaacttgtccatttcttgtcattgagtttctataccattgtggatttgaatggagtaggcataaaatttgtgggtt

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagt-agtaatgtcaacacttc--tgatattgt-catgtttcgtt--ttaagtttacactacaat-ctctttgggtctta--ttatgttatgttgtacacag---------------------------------
|| ||||||||| | || ||||| |||||||| || || ||||||||||||||||| || ||||| ||||| |||||  | ||||| |||||| | || |||   || | |   || | || |      || | || | | ||| | | |  |||  |   ||  |  || || |||   | | |   |   ||||  ||| | |                                   
CATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAAACAAGAAGACGTATAGgtagctacttaaccattttaaaatggaaatggtgtttttcctgtcttgctaattagttggtcataatgattctgtttcattatcaagcttgcttattctgtgctcgcattttcttgacatgtctgttataccatctccag

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S126_52V6.1 (Physcomitrella patens), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagttt---acactacaatctctttgggtcttattatgttatgttgtacacag
|| |||||||||||||||||||| |||||||| ||| ||||||| || ||||| | ||| ||||| |||||||| ||| | || |  ||||||||||  |||||| | |   |  |            || | || |      ||      |||   || |||  || | | ||       | |   || |   |     |
CATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagca-tcccaccgctgtattggtgaatttggttacaaactgtccgttatttgagactctatgatatgtgtgacagcggtaaccctaggacctttggtg

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S21_106V6.1 (Physcomitrella patens), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtag-taatgtcaacacttctgatattgtcatgt-ttcgtt--ttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag
|| ||||| || || ||||||||||||||||| ||| |||||||||| ||||| | ||| |||||||||||||| ||  | || |  ||||||||||  ||| ||   |||    ||| | |     |  | |  | |||  || |||  |||| ||   | |  |||| |    |   | | |  ||  |      || ||
CATAACAACGTCATTCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACTTGGTTCAACCAGCCCGCACGCAAGAAAAGAAGAAGAACGGgtgaggtttaggctttgttatcctccgtcttttgattatggattagttaattaatttagtaatgaaatcccacgcgtgatcaatgcgtc-tacaac-catag

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S459_9V6.3 (Physcomitrella patens), 5'ss of exon 1
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgt-tagtagtagtaatgtcaacacttctgatattgtca---tgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag
|| |||||||| |||||||| ||||||||||| ||| |||||||||| ||||| | ||| |||||||||||||| ||  | || |  ||||||||||  ||| | || ||  |  | |    | || || | || | |   || | ||       |||  |  ||| |   | |   | |  || |  ||  | | || || 
CATAACAATGTCATCCCCAACGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCACGCAAGAAGAGAAGAAGAACGGgtattgtcgtgcttttctgtgaagttttgtttttatgacggtggtacgggcgttttttggaacacagttcttgtccatgtgtttcttataactcgaac-ca-

upper sequence: AT3G49010.5 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S58_38V6.1 (Physcomitrella patens), 5'ss of exon 2
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattg-tcat--gtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag-
|| || |||||||||||||||||||||||||| ||| |||||||||| ||||| | ||| |||||||||||||| ||| | || |  ||||||||||  ||| | || ||||  | ||    ||||    |||| |  |  | ||    |||       | |  ||| | ||||      |  || | |     ||   |  
CATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgtaacta-tagttttttcggatcttcctgaattggttgttagctttcccttattacggaagtgtaatttttttgt-ctggaacatctcaaaccctatgaatt

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|124977541|gb|EL050852.1|EL050852
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|124855932|gb|EH940369.1|EH940369
EST:     GTCAAGTACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTT
genomic: GTCAAG-ACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTT
EST: gi|86018575|gb|DR314321.1|DR314321
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|124954575|gb|EL029658.1|EL029658
EST:     TCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|125048447|gb|EL120716.1|EL120716
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCT
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCT
EST: gi|125291489|gb|EL305574.1|EL305574
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAG
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAG
EST: gi|125222104|gb|EL236189.1|EL236189
EST:     TTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|164017344|gb|EL974819.1|EL974819
EST:     GCCAGGAAAACCNGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: GCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|86018573|gb|DR314319.1|DR314319
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|152037762|gb|BP796635.2|BP796635
EST:     TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
genomic: TGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCGTCCAACTTCTGGACCTC
EST: gi|124749000|gb|EH839130.1|EH839130
EST:     GTCAAGTACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTG                         CGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCG
genomic: GTCAAG-ACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagta ... ttgtacacagCGAGGCAAAAGAAGGCTGTGAAGATCTTCCCTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAGGAAAACCAGAAGAAGAATTGgttagtagtagtaatgtcaacacttctgatattgtcatgtttcgttttaagtttacactacaatctctttgggtcttattatgttatgttgtacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG