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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagcttcactctttagtttgataaagatttggattcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG

Basic information

species Arabidopsis thaliana
transcript AT5G60340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G27430.1 (Glycine max), 3'ss of exon 2
gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagcttcactctttagtttgataaagatttggattcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG
                                                            ||| |    ||  ||  ||| | | | |   |  ||   ||| | |  || || ||       ||   || ||  ||  |  |||| ||| || |   |||| | |  |     |||||| ||||| |||| ||||  ||| || || |||||||||||||||||||||||||| ||||||||| |||| ||||||||| |||| || |
------------------------------------------------------------tttaa--tattaatattatcctcatcattgatacttttcttg-tcatcatgtgtatgttgcctgatttat-aggttttatgtctattttgcatggtttttgtagGTTTG-----TGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCTGAGCGTTGGTTTGATTGCGTGGTTG

upper sequence: AT5G60340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G08350.1 (Glycine max), 3'ss of exon 2
gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagc-ttcactctttagtttgataaagatttggattcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG
                                                                     ||| ||  ||| | | | || || | ||  | |  | |   | ||  | |     ||   ||  |  |  ||  | |  ||   ||| |    |     ||||   |||||| ||||| |||| ||||  ||| || || |||||||||||||||||||||||||| ||||||||  |||| ||||||||| |||| || |
--------------------------------------------------------------------tttgatattatcctcatcattgacacatt--tcttgtcatcttgtgtgtgctgcctgatatataggtttattttacgagtttaatttgcatggtttctgtagGTCTGTGATGAACTTGAGGATGTTATGGAAGAGGGGGGAAACATTGTGGACTACCATGGCTGTGATTTCTTTCCCGAGCGTTGGTTTGATTGCGTGGTTG

upper sequence: AT5G60340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G33100.1 (Glycine max), 3'ss of exon 2
gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagcttcactctttagtttgataaagatttgg--attcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG
                                                               |      ||  | ||| ||||  || |  ||     |||| | |  | | |  ||    ||          |  || || ||| ||    | |  |  ||| | || |     |||||| ||||| |||| ||||  ||  || || ||||||||||||||||||||||| |  ||||||||| ||||||||||| || | || || |
---------------------------------------------------------------ggttacatgaaataattttaatatt-atcctcatcattgacacatttcttgtcatcatgtttatgtttcctgatttattggctttaca--actatatctgtagGTCTG-----TGATGAACTTGAGGATGTTATGGAAGCGGGGGGAAACATTGTGGACTACCATGGCTGCGTTTTCTTTCCTGAGCGATGGTTTAATTGTGTGGTTG

upper sequence: AT5G60340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g03280.t01 (Vitis vinifera), 3'ss of exon 1
gttagtttcttactccatccctatccctttatcctccttatttccttgtcaacaaaacactttgaaccgttgctagaatcttaagcttcactctttagtttgataaagatttggattcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG
                                      ||| ||  |||       |  |||   | | ||  ||||||   |    ||| ||         |||   || |  ||||  || |   |||       ||| |  || |||| | |   |||     ||||||   |||||||| || |||   |||  |||||| || |||||||||||||||||||| ||||| ||||| ||| |||||||||||||||| || || |
--------------------------------------tatctcactgtttg----atgctt---atcttttgtagaattacag---tcaatc---------atatgcatcttaattccctttgttaaat-------cttcgacattttgtgtggtttttg-----cagGTGTGCGATGAGCTCGAGGATTTGATGGAAGAAGGGGGAAACATTGTGGACTACCATGGTTGTGATTTCTTCCCTGAGCGATGGTTTGATCGTGTGGTGG

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|19877605|gb|AU238436.1|AU238436
EST:     ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCG                         GTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
genomic: ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCGgttagtttct ... tgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
EST: gi|47829067|gb|CK118751.1|CK118751
EST:     ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCG                         GTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
genomic: ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCGgttagtttct ... tgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
EST: gi|47827879|gb|CK117563.1|CK117563
EST:     ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCG                         GTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
genomic: ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCGgttagtttct ... tgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
EST: gi|301503180|gb|HO208720.1|HO208720
EST:     ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCG                         GTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC
genomic: ACCATGGCTGGGACAATGAGCTCGAGTGTCACTTCATCAACGAAGACTCGgttagtttct ... tgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaattcgaagaattagccttcttagctatattgtattgaacttgtggatcagGTGATTGATGAGCTTGACGATGCTATGATAGAAGGAGGGAACATTGTGGACTACCATGGCTGTGACTTCTTTCCTCAGCGATGGTTTGATCGCGTTGTCG
                             tatattgtattgaa  TA-rich tract