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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT4G12590.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 3
-----gtgagttgtatttgaaatg--tttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
     ||   ||  |||| || |   || |||||  | |     |   ||| | | | || |   || |     | |  ||||| |||||||| || ||||||||||| ||||||||||| || || ||||||||||
gttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgct-----tcaatatttttcagACACTTACATTTGCATGGGTGAACTTCTTCTTTTCGGGTTTTGTTGCAG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 3
-----------------gtgagttgtatttgaaatgtttcatctatgtttttgcgttac---tggtcatttaagaaactgatatca---cttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
                  ||| ||   | ||      |  |  |   |  | | ||  |       | | |   | | | | ||||   |||    ||||||||||||| || ||||||||||| ||||| ||||| || || || |||||||
gttctgtgttccgtacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatattaacatcataacttgtgtttttgcagACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 3
gtgagttgtatttgaaatgtttcat--ctatgtttttgcgttactggtcatttaagaaactgata-------tcacttaccattttg--cagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
  |  |||   | |   | ||   |  ||||  |||   || |  | |||  | |  |||   ||       |   ||||| || ||  ||||| || |||||||| ||||| ||||| ||||||||||||||||| ||||
--gtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 3'ss of exon 3
gtgagttgtatttgaaatgtttcat---ctatgtttttgcgttactggtcatttaagaaactgata-------tcacttaccattttg--cagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
  |  |||   | |   | ||||     ||||  |||   || |  | |||  | |  |||   ||       |   ||||| || ||  ||||| || |||||||| ||||| ||||| ||||||||||||||||| ||||
--gtattgctgtcggtgtttttctgttgctattctttaatgtaatagatcagatgactaaccattaattactgttttttacccttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16068 (Selaginella moellendorffii), 3'ss of exon 3
gtgagttgtatttgaaatgtttcatctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
          ||||   |      || |   | |||  |    |||| |  |   ||||  |    | |  | ||||||||||  | || ||||| ||||| |||||||||||||| ||||||||  | |
---------gtttggcgt------tccaaaatcttgtctc---ggtc-tcgagccaacttttcgggcgtttc-ttttgcagACTTTAACCTTTGCGTGGGTGAACTTCTTCTTCTCCGGATTTGTCACCG

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|124842454|gb|EH926891.1|EH926891
EST:     ATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAGCTTCTTCTTCTCTGGATTTGTTGCAG
genomic: ATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
EST: gi|164053653|gb|ES045035.1|ES045035
EST:     GATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
genomic: GATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
EST: gi|125011977|gb|EL084246.1|EL084246
EST:     ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACT
genomic: ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACT
EST: gi|86079343|gb|DR375100.1|DR375100
EST:     ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAG                         ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgta ... cattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcagACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG
                                      cacttac  putative branch site (score: 2)
                                            ccatttt  CT-rich tract
                     atttaagaaa  TA-rich tract