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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgttaaattaccggcaggatttgcgataaacttgtttacttttgccattaagatataaatttatttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT

Basic information

species Arabidopsis thaliana
transcript AT4G39520.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 7
--gtaaatgttgttaa-attaccggcaggatttgcgataaacttgtttacttttgccattaagatataaatttatttatctt----------gcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
  |  ||| |  || | ||     |  |   ||      |     ||| ||    | | |||   | |   |   ||  |||           |||||| ||||| ||||||||||| ||||| ||||| || | ||| ||||||||| ||||| |   | | || ||||||||||| || |   | || || |||
gtgagaatttaattgacatcttttgttgtgctttattccattcattttgctccaacaagtaaagcagactctccctttccttttatttgtccacagTGCTCATCTTGAGTGGAATCTCGATGGTCTTCTAGAGATGATCTGGGAATACCTGGATTTGGTTAGGATATACACAAAACCGAAAGGTTTAAACCCAGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------gtaaatgttgttaaattaccggcaggatttgcg-at---aaacttgtttacttttgccattaagatataaatttatt----tatc-ttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
                                                                    |  |      |||| |  |    | | |||  ||    ||| ||   |   ||   | |||||       || ||    |||  ||||||||| ||||| || ||||||||||||||||||||||| ||| ||||||||||||||||| |   | | || ||||||||||| || |   |||| || |||
gtgagcatgtactgtagtatcctgctgcaattgattcacttgatttcccttaatagctgaaacacctcatttaaaaaaaaatcattgcagtgctctgctcatctagaacctgaacatgcttaggactaagaggctttgttgttgttgtattgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 7
---gtaaatgttgttaaattaccggcaggatt--tgcgataaacttgtttac-------ttttgccattaag---atataaattt--atttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
   || |   ||     ||| | |    ||||  ||| ||||| || || ||       ||||   | |||     | ||| |||  || |||  | |||||| |||||||||||||| |||||||| |||||||| || || ||||||||  |  |  ||||||| || || || ||||| || |  |||||||| |||
actgtcacgtttcccccatttctgttgtgatttttgcaataaatttattcacaaagttgttttcttaataaatatgtgtaattttctatctatgcttcagTGCACATCTGGAGTGGAACCTTGATGGTCTTCTGGAGAAAATTTGGGAATATCTCAACTTAACTCGTATTTATACTAAACCTAAAGGGATGAATCCTGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 7
-----------------gtaaatgttgttaaattaccggcaggatttgcgataaacttgtttacttttgccattaagatataaatttatttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
                   ||||  | |||   ||         ||   | |   | | | | | |||    ||  | | | |  | |||  |  |||||||| || ||||||||||| |||||||| || || || ||||||||||| ||  | ||| ||||||| || |||||||| || |||| ||||||||| |||
tggtgtcattgtttttgccaaataatcttattctagtcattcatttgaggtttttcatttctccctttttggttgtggtttgatatgattattgctgcagTGCTCACCTGGAGTGGAACCTTGATGGTCTGCTAGAAAAGATATGGGAGTATCTTGATTTAACTCGCATATACACAAAGCCCAAGGGAATGAATCCCGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S26_115V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------------------------gtaaatgttgttaaattaccggcaggatttgcgataaacttgtttacttttgccattaagatataaatttatttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
                                                                                                                           || ||| |  |   |  |  | ||  ||  | |   ||  || | |  ||    |||   |||    | | | | | ||| ||||| ||||| |||||||| || ||||||||  |||||||||| |||||||||||| |||| |  ||| | ||||| ||||| ||||  |  |  || |||
gtattgaaagatattatattcaagagttttgtttttgatgtggattttagaatggttgctcttctattatgcttgacgaatgtatgttgatgcattgctagtgatggaggaagttgtattgttgtgaatctattctga--attgacatcatcggaggagaaggtgctcagctt----attcttatacttctgt-tctgttttgaagTGCCCATCTTGAGTGGAACCTGGATGGACTCTTGGACAAGATTTGGGAATACTTGAATCTTATCCGAGTATACACCAAACCCAAGGGCAACAGCCCCGAT

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|125273571|gb|EL287656.1|EL287656
EST:     CTTGAGGAACTTGAAATTTTGGACAAACTTCCTCATTACTGTCCTGTCAG                         TGCGCATCTGGAGTGGAATCTTGATGG
genomic: CTTGAGGAACTTGAAATTTTGGACAAACTTCCTCATTACTGTCCTGTCAGgtaaatgttg ... tatcttgcagTGCGCATCTGGAGTGGAATCTTGATGG
EST: gi|47830368|gb|CK120052.1|CK120052
EST:     CTTGAGGAACTTGAAATTTTGGACAAACTTCCTCATTACTGTCCTGTCAG                         TGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATA
genomic: CTTGAGGAACTTGAAATTTTGGACAAACTTCCTCATTACTGTCCTGTCAGgtaaatgttg ... tatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATA
EST: gi|125247899|gb|EL261984.1|EL261984
EST:     TTGAGGAACTTGAAATTTTGGACAAACTTTCCTCATTACTCTCCTGTCAG                         TGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGG
genomic: TTGAGGAACTTGAAATTTTGGACAAAC-TTCCTCATTACTGTCCTGTCAGgtaaatgttg ... tatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGG
EST: gi|86080003|gb|DR375760.1|DR375760
EST:     TCCTCATTACTGTCCTGTCAG                         TGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATA
genomic: TCCTCATTACTGTCCTGTCAGgtaaatgttg ... tatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgataaacttgtttacttttgccattaagatataaatttatttatcttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
                                           tttatctt  CT-rich tract
              tttacttttgccatta  TA-rich tract