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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaacttaaatcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT

Basic information

species Arabidopsis thaliana
transcript AT3G27090.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
gtgaaacttaaatcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT
            | |||     | |||||   || | || | ||||   | |  |    |  | | || | |   ||    |   |   |||| |||||| |  | |||||  | |||||  | ||||||||||| ||||||||||||||  | ||||| |||||||| ||||| ||||||||||||||||
-----gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttc----accatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 4
gtgaaacttaaatcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT
            |    || || |   |  || |  |  ||| |    || || | |  |    |    |||  | | |  ||  |  ||||| |||||| | || |||||  | |||||  | ||||||||||| ||||||||||||||  | |||||||||||||| ||||| || ||||| |||||||
-----------gtactgataacatctgtcattatgtgcatttctc---atctcctttggtttcttg--ctctgacaccttcatcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCT

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
-----------------------gtgaaact-taaatcacaat--gactttcattgttttaagtctttattttgatatcttgta--ctaata--taacttctttctcttaaattg-taacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT
                       || |||   | | ||||  |  | |    |    ||||| |  |   |   | || |  ||    | |   || |  ||   | || | |||     ||||  |||   |  |  | ||    || ||  | || ||||||||||| ||||||||||| || || ||||||||||| || || ||||| ||| ||||||
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT

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|125038979|gb|EL111248.1|EL111248
EST:     ACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAG                         GTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTC
genomic: ACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGgtgaaactta ... attgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTC
EST: gi|125068830|gb|EL134820.1|EL134820
EST:     AGTCAAGGTTTCCGGCTCAG                         GTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTC
genomic: AGTCAAGGTTTCCGGCTCAGgtgaaactta ... attgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTC
EST: gi|125166573|gb|EL192306.1|EL192306
EST:     GGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGTCTCAG                         GTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTT
genomic: GGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGG-CTCAGgtgaaactta ... attgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTT
EST: gi|125320478|gb|EL334563.1|EL334563
EST:     TGCAAAGGAGAGTCAAGGTTTCCGGCTCAG                         GTTAAGGTATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCT
genomic: TGCAAAGGAGAGTCAAGGTTTCCGGCTCAGgtgaaactta ... attgtaacagG-TAAGG-ATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCT
EST: gi|124732253|gb|EH823655.1|EH823655
EST:     CTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAG                         GTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAG
genomic: CTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGgtgaaactta ... attgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAG
EST: gi|125018961|gb|EL091230.1|EL091230
EST:     CTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAG                         GTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGG
genomic: CTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGgtgaaactta ... attgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT
                       taatataacttcttt  TA-rich tract