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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag

Basic information

species Arabidopsis thaliana
transcript AT1G27400.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag
||||||||||   ||| |||||||||||| | ||  |||||||||| ||||| || |||||||||||||||  |  ||     |   |        | | | |      |||  |  || || ||  |   |  |  ||  | ||| |   || ||| | |||   
CTTACATGTCCTCCCCGTGCCACATTGAGCTTATCCTGTCAGAGAAGGAAGAACCAGTGAAGAAAGAGgtatgtgcatctgtaccttgagaagtccattgtataagctaactgctggttgatgtttttttttattaccatctgattgtgaatgtgttat-gcag--

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G702426_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatt----------taatgatcccaacg----cctctctgaatatcttcaaatacttatatttcat--cttcatcactgatct--cacataatttttgttgggttct-tgcacag-------------------------------------------------
||||||||||   ||| |||||||||||| ||||| |||||||||| |||||||||||||||||||||||| ||          |||  || |||||       | ||||| ||||||  | |  |   ||||||   ||  ||   |  |||   ||| || | |  ||   || | ||  |                                                   
CTTACATGTCCTCCCCTTGCCACATTGAGCTGATTCTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtatttaacatgctcataaaaatgccaactagatattttctgagtatcttgcattgatctaatttcagagctgtattgttcttctggtacagaagtatccttccattttatgttctttccatttgaatagtatctgtctgtaatatatgtcatctttattttgtag

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G148744_T01 (Zea mays), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaattta-atgatc-ccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcaca-taatttttg--ttgggttcttgcacag--
| ||||||||    || |||||||||||| |||| ||||||||||| |||||||||||||||||||||||| |  | ||| ||  |||   |  |||  |||| ||    |      || |    ||  ||  | || ||| |   |||||||  || |||||||        
CCTACATGTCCTCACCTTGCCACATTGAGCTGATCTTGTCAGAGAAGGAAGAGCCTGTGAAGAAAGAGgtattacacatgttcatcaaatgccatctatatattttt---tctgagcatcttgcattggtc--taatttcagagctatttttggcttaggttcttatggtaca

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G127521_T01 (Zea mays), 5'ss of exon 5
--------------------------------CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttg---ggttcttgcacag
                                ||||||||||   |||||||||||| ||| | || ||||| ||||| |||||||| |||||||||||||||  |  |  ||      |  |       |       | ||| |  ||||  |       | | || |      ||| | ||     | ||| |   |||
AGCTTAACATTCTGTTTGCCTACCTGGTCCAGCTTACATGTCCTCCCCATGCCACATCGAGCTCATCTTGTCGGAGAAGGAAGAGCCAGTGAAGAAAGAGgtatgtggac-atgtggttgtgtacactgttgcacctgattacctg-atttagtgcatgggattaatgttgtgctattgtggtcaatcgtttccttttcag

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 5
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctct--ctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag
||||||||||   ||| |||||||| ||  | || ||||||||||| |||||||| ||||||||||||||| ||   |     ||  |  |    |||| |||||      ||| | |        | |    || | |   ||  |  |  || | ||| |   |||
CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctg-----actgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcag

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G119169_T01 (Zea mays), 5'ss of exon 7
--------------------------------CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctct--ctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag-----
                                ||||||||||   ||| |||||||| ||  | || ||||||||||| |||||||| ||||||||||||||| ||   |     ||  |  |    |||| |||||      ||| | |        | |    || | |   ||  |  |  || | ||| |   |||     
TTGCAGCTTAAGATCCTACCTACCTGGTGCAGCTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggttttgtacactgtttgcacctgattatctg-----actgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcaggctga

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G126594_T01 (Zea mays), 5'ss of exon 5
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttg---ggttcttgcacag
||||||||||   |||||||||||| ||| | || ||||| ||||| ||||| || |||||||||||||||  |  |  ||      |  |       |    |  | ||| |  |||   |       | | || |      ||| | ||     | ||| |   |||
CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAGgtatgtggac-atgtggttgtgtacactgttgcacttgattacctg-attcagtgcatgggattaatgttgtgctattgtggtcaatcgtttccttttcag

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G37160.1 (Glycine max), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaat--ttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag
|||||||||||   ||||||||||||||| |||| ||||| ||||| ||||||||||||||||||||||||||  || |  ||| |   |  |  | | |||| | |     ||| | |||    |  |   || ||||   ||  || |||| |             
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAGgtaatgattgaccatctctctgt-taacagtatatatacttcctcttttcttttgcatcaaattcttatctattattgttcttgtag-------------

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G01110.1 (Glycine max), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag
|||||||||||   ||||||||||||||| |||| || || ||||| |||||||| |||||||| ||||||||  | ||| |       ||||||||  |  ||  | |   |   | |  ||||   ||   |  ||  ||   | ||||||   ||||| |   
CTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAGgtaatg-attgacc-----atctctctgataacattatattgacttcctcttttcttttgcatcaaattcttat--ctattgttg--ctcttgtag--

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G27940.1 (Glycine max), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatc-ttcatcactgatctcacataatttttgttgggttcttgcacag
|||| ||||||   || |||||||| |||||||| || || || |||||||| ||||||||||| |||||| || | | |||     |  |   |||   ||| |     ||| | ||  ||  ||||| |   |  ||  ||  ||||| |||| || | |     
CTTATATGTCATCTCCGTGCCACATAGAGTTGATATTATCTGAAAAAGAAGAACCTGTGAAGAAGGAGgtatttgattcatcta---gttttgttgatcctctcccccccctttttttcaatgattcattatctaattcctattcttttt-ttggtttgtag-----

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 5'ss of exon 5
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctc--------tctgaat--------atcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag
| || ||||||   |||||||| ||||||||||||||||| || || ||||| ||||| || || ||||||||| | |  ||    |  |           |  ||         || |   |  | |||  |  | |  |  | | |  | ||  |  | | ||| |||||| |||||   
CATATATGTCATCACCATGCCATATTGAGTTGATTTTGTCTGAAAAGGAAGAACCTGTTAAAAAGGAGgtaattcattagtcattgcatcaagaatagaacccaaagggagagcaatataggagaaattagttgccctggttttgattagtatcttactactcttggtgggtt-ttgcag--

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S38_376V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag---------------------------------------------------
||||||||||    || |||||||||||| ||||  | || ||||| |||| ||| ||||||||||||||||||| | ||| | ||      |   || |  || | ||| ||   | || | ||  ||  |  | |  | | | | |   |      ||  ||||                                                   
CTTACATGTCCTCTCCTTGCCACATTGAGCTGATCCTTTCTGAGAAGGAAGCGCCAGTGAAGAAAGAGgtaatttta-gatgctaaattagatggcaaaagttttagatagtttcctgtcctgtttttcgattttgtttcgtgactgtaaattcacaatt-tacagttatttataattcagaactgtaaattaaccggttctttacgggctttgcag

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|124921521|gb|EH995130.1|EH995130
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAG
EST: gi|47827860|gb|CK117544.1|CK117544
EST:     GCCACATTGAGTTGATTNTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGTCTCATC
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATC
EST: gi|124742356|gb|EH833518.1|EH833518
EST:     GATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAAGAAAGGAGCCTCATCTTAAGC
genomic: GATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAA-GAAAGGAGCCTCATCTTAAGC
EST: gi|164175725|gb|ES163433.1|ES163433
EST:     AAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGTCTCATCTTAAGC
genomic: AAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGC
EST: gi|86074318|gb|DR370075.1|DR370075
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGCT
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGCT
EST: gi|124761331|gb|EH851461.1|EH851461
EST:     CCACATTGAGTTGATTTTGTCACGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAA
genomic: CCACATTGAGTTGATTTTGTCA-GAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAA
EST: gi|164221496|gb|ES123118.1|ES123118
EST:     CTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGTCTCATCTTAAGCT
genomic: CTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGCT
EST: gi|124931215|gb|EL008592.1|EL008592
EST:     GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAG
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAG
EST: gi|116444090|gb|EG486682.1|EG486682
EST:     GCCACATTGGGTTGATTTTGTCAGAGAAAGAAGAGCCCGTGAAGAAAGAG                         CCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGCT
genomic: GCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaat ... tcttgcacagCCGGAGACACAGTTGGCAGCAAAGTCAAAGAAAGGAGCCTCATCTTAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAGgtaatttaatgatcccaacgcctctctgaatatcttcaaatacttatatttcatcttcatcactgatctcacataatttttgttgggttcttgcacag

- - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA