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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC

Basic information

species Arabidopsis thaliana
transcript AT5G55280.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattg-atccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
                                         | | || ||| ||   |      |   |  || |||  | ||| ||   || |      ||| |||||||||||||| |||||||| |||||||| |||||||| || || |||||| | ||||||||||||||||| || || |||||||||||||||||||| |
---------------------------------------gtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
                           |     |||  |              | | | |||  ||||  || | |  |   |   |||   |     ||   |||||||| ||||| |||||||| |||||||| ||||| || || ||||||||| | ||||||||||| |||||||| || |||||||||||||||||||| |
--------------------------gtgggtggtttctcccctttcctgctctaacttatctgcaaa--ttgttatcatgtaccttatgagtgaacattg--cagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 4
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtata-tattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
       | |   |  || |  |  |||      || |   ||  |||   |  |  ||  |    |   || |    | |||||| | |  | ||   | || ||| |||||||||| ||||||||||||||||| ||||| || || || |||||||| ||||| ||||||||||| || ||||||||||| ||| | |||||||
----acttctccttcata-attgggcattgtggctttgc--atttatgtcaagggtatgtccatggatttttttctcaacacagtaaactggtgtgccttcttgcagGTACCTGGACTTGTCAATGTAGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGTGTAGGTGTTTCATCCGGTAAAAACC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtata---tattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
     ||  |   |  || |  |  |||      || |   ||  ||| | |  | |   |||       || |      ||| ||||   | || ||   | || ||| |||||||||| |||||||| |||||||||||||| || || || |||||||| ||||| ||||||||||| || ||||||||||| ||| | |||||||
-----tcacttcttcata-attgggcattttggctttgc--attcatg-tcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 5
gtgagtctatgtattgtataaagcacataacaagttggttgatg-aatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
     | |  || |||         |||||   |    || ||| || |   |||  |||||  |     ||   || |  |     | |    |||  |||| ||||||||||| || || ||||| |||||||| ||||| || || || |||||||| ||||||||||||||||| || || |||||||| ||||| |||||||
-----tttcagtgttgctcctccatcataattggacaattaatgtaaagtacatt--ttgatgtcagcttatcaggatgttattcagtgttacgtgtctttttacagATACCTGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCAATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtata-tattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
     | |  || |||         |||||   |    || |||||   | |    |||||  |   || || |||||| |   | |  | ||   |  |||| |||||||| || || || ||||| |||||||| ||||| || || || |||||||| ||||||||||| ||||| || || |||||||| ||||| |||||||
---tatttgagtgttgctcctccaccataattggacaattaatgaaaagt-acattttgatgtc---agcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4
-gtgagtc--tatg-tattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
  ||| |   |||| |||| |    |  |  |  |||    |  | | | |  ||  || |||||||   |  |||      ||| ||  | |  |    | |||| |||||||| || || || ||||| |||||||||||||| |||||||||||||| || ||||||||||||||||| || || || |||||||||||||||||||
actgatttattatgatattttcctgattaatttccaatactgaagttta-tctttgctg-ttgatcctatataattt----aaaatagcgtgtcct----tgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

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|124784051|gb|EH873823.1|EH873823
EST:     ATATTATTACT                         ATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAA
genomic: ATATTATTACTgtgagtctat ... tctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAA
EST: gi|86039265|gb|DR335020.1|DR335020
EST:     CAGATGATGTTTTACGCCAAGGAGTACAAGGAATCTCAGATATTATTACT                         ATACCTGGACTAGTCAATGTGGATTTTGCAGATGTGAAGGCAGTCATGAAA
genomic: CAGATGATGTTTTACGCCAAGGAGTACAAGGAATCTCAGATATTATTACTgtgagtctat ... tctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC
                                     tattttgttctttttc  CT-rich tract
                               agtatatattttgttc  TA-rich tract