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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacattttgtatttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT

Basic information

species Arabidopsis thaliana
transcript AT1G48110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 4
gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacattttgt-atttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT
           |    |  ||   ||    || | ||  || |||  | |||   |  ||     | |||  ||| || ||| || |   |  ||||||||  || || |||| || ||| |||||||  ||||||||||| ||||||| |||||||||||| || ||||||| ||||||||| || ||||| ||  
-----------gtgagtctagttctcct-ctacttgtgtatatgtg-tcatatgctgggttgaaagctgatttga-atgcttgttct---ttgccagGGTGCACAAAACGAAAGTTTTCCATATATATATTATACACCTAGCTATGGATTTGCACAGTCTCCATACAATCCATACAATCCTTATATTCCTGGTGCAA

upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G14490.1 (Glycine max), 3'ss of exon 4
gtactaatctcggacataaagacttctcattaatcgttgatttgttc--ttatacattttgtatttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT------
                        |    |||| |  || ||   ||  |  ||  ||  ||  | | |||  |  |||  || | || ||| | |||||||  || ||||||| || ||| ||| |||  ||||      | |||||||||||||||||||| || ||||||| |||||||||||| ||||| |||       
-----------------------gtaagtttaacctctgtttcactctatcctaagttgggtcatggctgatttt-tatgtttctgtt-ttttttcagGGTGCACAAAATGAAAGTTTTCCGTATGTATATTATA------GCTATGGATATGCACAGTCTCCATACAATCCATACAATCCTTACATTCCTGGTGCTATGATTG

upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacattttg-tatttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT------
           | |  |  | ||||||   |  |  || | |   | |  ||  ||  |  | | | |||  |  |||  || |  | ||| | |||||||  || ||||||| ||  || ||| |||  ||||        |||||||||||||||||||| || |||||||  ||||||||||| ||||| |||       
-----------gtaagttta-acttctgtgttctgtttcactctatatcctaagttggggcagtggctgatttt-tatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG

upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
---------------gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacat-----tttgtatttgttgacatgatatcc-tttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT
                   || | ||       ||  ||  | | ||   |||   |  ||||| ||  |     |||||  |||||  | | || |||   || || || || ||||||| ||| | ||| | ||  || ||| |||  ||||||||||| ||||||||||||||||| || || || |||| |||||||||||||||||| ||  
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttcttttagttgatcatttgtgattgtt--cgtaatgtccaccttcttcttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA

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|116428293|gb|EG470885.1|EG470885
EST:     AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAAAAGTCCAATACACA                         GGGGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
genomic: AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACAgtactaatct ... gtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
EST: gi|116434950|gb|EG477542.1|EG477542
EST:     AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACA                         GGTGGGCAGAATGAAAATTCTCCCTATATATGCCATACACCTAGTTATGGA
genomic: AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACAgtactaatct ... gtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
EST: gi|125287197|gb|EL301282.1|EL301282
EST:     GGTGTAGATGGTTCAGAAGTCCAATACACA                         GGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACA
genomic: GGTGTAGATGGTTCAGAAGTCCAATACACAgtactaatct ... gtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACA
EST: gi|116403222|gb|EG445814.1|EG445814
EST:     AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACA                         GGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
genomic: AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACAgtactaatct ... gtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
EST: gi|116437119|gb|EG479711.1|EG479711
EST:     AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACA                         AGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA
genomic: AGAACCATCAGATGTTTTTTGGTGTAGATGGTTCAGAAGTCCAATACACAgtactaatct ... gtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcttatacattttgtatttgttgacatgatatcctttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT
                      tgttgac  putative branch site (score: 3)
                                 tatcctttttttgttt  putative PPT
      ttatacattttgtatt  TA-rich tract