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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag

Basic information

species Arabidopsis thaliana
transcript AT2G44610.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag
|| ||||| |||||||| || || |||||||||||||||||||||||| | || |||||||| ||  | ||||| |||        |   |  |||| |   || |         | |||   |||         |   | |        |      |  |    |||
GCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTGgtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag
|| ||||||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | |||||  ||    |  ||  | ||    |      ||| |      |||||      |      | |||       |  | |  |   || |    |||
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattacta--ctactgcatccgttagc--ctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttcttt--gcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgaga--gccgaaatcatatgacag
|| || |||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | ||||| | |     | ||  | |    |||  |  |||     |  |  |  |||||   | | ||   || || |   |   |    | |    |  |||
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggt-----gactactactgcattcatagcctgtt---tgccccttgagatc---tatggactgttgaccttatgcatgttttattttctttgcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcct-ctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag--
|| |||||||||||||||||||||||||| || ||||| |||||||||||||| ||  |||| ||||||||||||||| | |  ||  | |   ||  |   |   | ||  |||| || |      | |       | || |      ||   |||    || ||     
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatatgggaccagcatctcatagtaatagtataaattataaaatggtcaggaaatgaaaagggttttaggaaaggattggaagaagtaggatcatg

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag-----
|| |||||||||||||||||||||||||| || ||||| || ||||||||||| ||  |||| |||||||||||||||   |  ||    ||   |     | | ||   |  ||       |    ||     | ||||   |     ||  ||||||||  |   |     
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatacaggaccaacatctcatagtataaattgctcaggaaatgaaagggcttttaagaaaggattggaagaagtag--gaaatcatgggtgggatagt

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgat-taacatcgagagccgaaatcatatgacag-------
|| ||||| ||||| |||||||| ||||| || ||||| |||||||||||||| ||  |||| ||||||||||||||| |||   ||   ||| ||||  ||| |      | ||   |   ||  |||| |  |  |  | |      | |  | || |  | ||  |       
GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgttg---cttgatca-ttttaaaattccactaga-aagggtatggaatatttgtgaagaaagtgatggaaggggaagcaaacgaaggattgcttggtc

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattt-tcgaatactgaagaataacattgcagatcattttttgatgattaac---atcgagagccgaaatcatatgacag--------------------------------------
||||| ||||||||||||||| ||||||| || ||||| |||||||||||||| ||  | || ||| ||||||||||| | |   ||     | | | ||  | |   || |||   ||||  ||  |       | |  |  |   |||  || ||   ||||||| |                                         
GCCACGATTGGTATTGATTTTTTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGGCTGCAGCTgtggtaagatgtggcatcttggaaattctatccgaaaggaaataatggtattggggacgaaaagggaagggattcccttatcttgatcccttatcatataatttaggagttatcttttattagggatttgacttgcaatcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagat----cttgagcctctttcaattttc-----gaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag
|| ||||| ||||| |||||||| ||||| || ||||| |||||||||||||| ||  |||| || ||||||||||||    ||||| | | ||  || ||||     | |   | | |||||    || |||  ||  |   | |   | ||  |          || |||     
GCTACAATCGGTATCGATTTTCTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAATTGTGgtaagatgttgcttgatcattttaaaaatttcactagggagggtaaggaatagttatgaagaaaatgatggaaggggaagcaaaggattgtttggtc-tat-----

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 2
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacatt---gcagat-cattttttgatgattaacatcgagagccgaaatcatatgacag
|| || |||||||| ||||||||||||||||| ||||||||||||||||| |||||| |  | ||  | |||| |||| || ||    |     |||     |  |     |||    |    || ||  ||||||   |     |  || | |      ||  | |||   
GCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt-agttcttgatgctttagacctgtttgtatatattgctcccacaaatatatttttgtctctcccatttcaaaaatatttattttctgaagt

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaag-atcttgagcctc--tttcaattttcgaatactgaagaataacattgcagatcattttttga--tgattaacatcgagagccgaaatcatatgacag--
|| || || |||||||||||||| || ||||| ||||||||||| ||||| || ||  |||| ||| | ||||||| |  || || ||   |||||  |  | |||  |    | | || || |    || || | |    |  ||   |  |          | |  |  ||  
GCAACCATCGGTATTGATTTTCTCTCTAAGACCATGTACCTTGAGGATCGTACCGTGCGACTACAGCTCTGgtaagtacgttcagactaagtttcagctcgccaatgat----atttacttttctctgcacttgtagggccggatatgcttcactttttcgtccctgaggaagtc

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 5'ss of exon 4
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag--------------------------------------------------------------------------------------
|| || ||||||||||||||||| || ||||| ||||| ||||| ||||| || || ||||| ||| | ||||||   | |       |    |||     | | |  ||  ||      |   | | |   | ||  |   | | |   | | || | |  |  | |                                                                                      
GCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTGgtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggc-aatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctcttt---caattttcgaatact--gaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag
|| || ||||| ||||||||||| ||||| ||||||||||||||||| || || ||  | || ||| | ||||||  |  | ||  || ||     ||||   || | |  | | | |  | | |     ||  |||    | || ||   |       |||  || ||    
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg--

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|164008413|gb|ES056055.1|ES056055
EST:     CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCT
genomic: CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCT
EST: gi|116467570|gb|EG510162.1|EG510162
EST:     CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
EST: gi|164055793|gb|ES099932.1|ES099932
EST:     TACCTTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAA
genomic: TACC-TTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAA
EST: gi|124916170|gb|EH990044.1|EH990044
EST:     CAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: CAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
EST: gi|125223275|gb|EL237360.1|EL237360
EST:     TCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: TCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag

- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGA