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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT

Basic information

species Arabidopsis thaliana
transcript AT5G10360.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
gtactagattccaccccattgataaaattatacagcttctctt--tttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
                   | | ||   | ||   ||  | ||   |||    || || |     |  | |    || | || |   |  | ||   ||| || ||||| ||  | ||  | || ||| |   ||| ||| | ||  | |||||||||||||||||||| || ||||  ||||| |||||| |||||||
------------------gtaaaaaggctctatttctattattgactttcggatattcatgcccttgctctgaccatattatgttacttgtatggc-agGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 4
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT-----------------------------------------------------------------------
                                                                | | |    || |||| ||   |||||||  ||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | ||||||||||||||||| ||||||||||  ||||| |||||| | |||||                                                                       
----------------------------------------------------------------tatctgaacatttgatatga--attgtgt--aggcactccctgcttccgcggttatggcaggcgtaatggtgagcgcaggaggaagtctgtccgtggttgtattGTGAGCCAAGACCTATCTGTTATCAACTTGGTAATTGTTAAGAAGGGTGAGAACGATCTGCCTGGTTTAACTGACACTGAGAAGCCAAGGATGAGGGGTC

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G054136_T06 (Zea mays), 3'ss of exon 3
gtactagattccaccccattgataaaattatacagcttctct-ttttttcatta--atctt---ctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
    |    ||||      |    | | |    |  | |  | |  | |||  |  |||||   || || || |||| |      ||    |    | | |||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | |||||||||||||||||||| |||||||  ||||| |||||| | |||||
---ttctgctccataggggtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
|||          |    |  |    | | | || |  |   ||||    | | |||| | ||    ||   |||    ||||           |||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | |||||||||||||||||||| |||||||  ||||| |||||| | |||||
gtatagagacttcctatgtccagtgtactct-caacaccatcttttactctgattcttatctgaacattcgatatcaattctg-----------tagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 4
gtac-tagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
|||  |||| |  | | |  |  ||   | | ||| |  |||||||     |   |||| | ||    ||  | || |||       |||||||  ||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | ||||||||||||||||| ||||||||||  ||||| |||||| | |||||
gtatatagactgtatctccattgtactctca-acaccccctcttttacctgtggttcttatctgaacatt--tgatatga-------attgtgt--agGCACTCCCTGCTTCCGCGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGTATTGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
||| ||||  |   || ||| | |   |  |       |  | |||| |  | ||  |      | | |    ||  ||| |   |  |||    ||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | |||||||||||||||||||| |||||||  ||||| |||||| | |||||
gta-tagagact-tcctatttacagtgtactctcagcaccatcttttactctgattct------tatctgaacattcgatatcaattctgt----agGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgtt-----ttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
     || |         ||| |       ||| |||| |   |     ||| || || |  ||      ||  |||| |||    || |||   ||   ||| |||||||||||  | ||  |||||||| | | ||||||| | ||  | |||||||| ||||| |||||||| ||||||||||| |||||||| |||||
-agtaaggtcatgtatatttgttttttaggtactgctttttcataaccaatttatgttattggtccaatgttaaatttctgtttgttgcttacc-tgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
------gtactagattccaccccattgataaaattatacagcttct--ctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
      |||||   ||       ||   |  | | |   | ||| |  |     ||  ||| | ||      ||    || || ||   || |||     |  ||| |||||||||||  | ||  | |||||| | | ||||||| | ||  | |||||||| ||||| |||||||| ||||||||||| |||||||| |||||
tttgaggtactg--tttttttttataactggactcaggaaacttttagccaacctttgttattttttcaatgttaaatttcatttg--ttgcttacc-catgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

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|116469836|gb|EG512428.1|EG512428
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|125037387|gb|EL109656.1|EL109656
EST:     CGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: CGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|124850736|gb|EH935173.1|EH935173
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTT
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTT
EST: gi|164114430|gb|ES068524.1|ES068524
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|116469839|gb|EG512431.1|EG512431
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|124805097|gb|EH892554.1|EH892554
EST:     CGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: CGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|124842392|gb|EH926829.1|EH926829
EST:     CGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: CGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|125315624|gb|EL329709.1|EL329709
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
EST: gi|164067972|gb|ES038829.1|ES038829
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGA
EST: gi|125206555|gb|EL221509.1|EL221509
EST:     GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGA
genomic: GAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGA
EST: gi|164222456|gb|ES108445.1|ES108445
EST:     GGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAG                         GTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA
genomic: GGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGCTTCACCGAGgtactagatt ... ttgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT
      cattaat  putative branch site (score: 3)
                     ttttttatttatgtga  TA-rich tract