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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttcacatttagtattttagtatccagtttttcggtttttctagtgttttctttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG

Basic information

species Arabidopsis thaliana
transcript AT4G14910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
-gttcttcacatttagtattttagt-atccagtt-tttcggtttttctagtgttttc--tttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG
   || |    || | | |    |  || |||   |||| |  ||   |     | |  ||   ||    |||    | | | | || |||       || |||| || ||||||||||| ||  ||||||| || ||||| ||||||||||||||||| |||
cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG

upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------gttcttcacatttagtattttagtatccagtttttcggtttttctagtgttttctttgtttgttaaaatcactaaatgactcttt------tcccattt--agTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG
                                                                        ||||   | |  | ||  |  ||||  | || | | |  || |    ||  |||| ||  |||  || |||||   || || |       | |||||  |||||||||| || |||||||| ||  ||||||| || ||||||||||| |||||||| |  |||
gtagtgtatgttgtttaattacttcattaaactttggaattttgctattgagcctctgatgtttccaaatactctttttaatgtgaatcatc-tatcatgcttcttgttccttttgtctttccctttattc-ttattattactaatgaaccctctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------gttcttcacatttagtattttagtatccagtt--tttcggtttttctagtgttttctttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG
                                                                          || || |  |  |  || ||     |  |||  ||| |  ||| |   | || |  || |||  |||    ||    ||  | |  ||   | ||||||||||| || |||||||| ||  ||||||| || ||||||||||| |||||||| |  |||
gtagtgtatgctgtttaattacttcattaaagtttagaattttgcctattgagcttctgatgtttccaaatatttttttaatgtgaatcatctttcatgcttgttccttttgtctttccctttattcttattatttactaatga-acctgctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 3'ss of exon 5
----------gttcttcacatttagtattttagtatccagtttttcggtttttctagtgttttctttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG
               ||| |  ||  || ||||      | || ||  || ||      |||  ||| | |  | |||   || | ||| | || ||  |||||||||||||| ||||| |||||||| |||||||||||||| || ||||| |||||||| ||||||
gacatctaaaaaaaatcataccta--atcttaggtattggattctcatttgtttatccttttaatttatctaatgaaa---ctcattgatttttatcatatttagTTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAG

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|86058153|gb|DR353910.1|DR353910
EST:     GATACAACTTAGAGATTCCAACTCAGAGAGTAGGAACATATGACACTCAG                         TTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTT
genomic: GATACAACTTAGAGATTCCAACGCAGAGAGTAGGAACATACGACACTCAGgttcttcaca ... tcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctagtgttttctttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG
                             cactaaa  putative branch site (score: 2)
                                       ctcttttcccattt  putative PPT
              tttgtttgttaaaat  TA-rich tract