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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaataaacacaagtttcttttatttttcctgttacttaaacaatttgatatgattgttctgaaaccgaatttaatttcttttgtcagACTGATGATCCTGCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCCACTCATGATCGGTTACTTTGCATTGTCTGTCCCATCAGGACTATCTATTT

Basic information

species Arabidopsis thaliana
transcript AT2G28800.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28800.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 7
gtgagaaataaacacaagtttcttttatttttcctgttacttaaacaatttgatatgattgttctgaaaccgaatttaatttcttttgtcagACTGATGATCCTGCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCCACTCATGATCGGTTACTTTGCATTGTCTGTCCCATCAGGACTATCTATTT---
        ||||||||    |  |    | || || || |||      |||| | | |        ||||  |||   | |||||||| ||||| |||   ||| | || ||||||   |||||| |||| |||||||||||||||||||| || |||||  |||| ||||||||||| |||||| | ||||   
-------gtaaacacatcagttctcctctgtttctttttctt---ttttttggtgttaac------aaactaaat--gacttcttttgacagACAGAT---CCTTCTCAAAAGAATCAACTTCTTATTTTAAAGTTTCTTCCACTCATGATTGGCTACTTCTCATTATCTGTCCCATCTGGACTAACAATTTACT

upper sequence: AT2G28800.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 7
gtgagaaataaacacaagtttcttttatttttcctgttacttaaacaatttgatatgattgttctgaaaccgaatttaatttcttttgtcagACTGATGATCCTGCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCCACTCATGATCGGTTACTTTGCATTGTCTGTCCCATCAGGACTATCTATTT---
        ||||||||    |  | |  | || ||||| |||       || | | |  ||  || ||        | | |||||||| ||||| |||   ||| | || ||||||   |||||| |||| |||||||||||||||||||| || |||||  || | |||||||||||||||||| | ||||   
-------gtaaacacatcagttctcttctgtttctgtttcttttttgtgtttacaaggctggcctaaa--------tgacttcttttgacagACAGAT---CCTTCTCAAAAGAATCAACTTCTTATTTTAAAGTTTCTTCCACTCATGATTGGCTACTTCTCACTATCTGTCCCATCAGGACTAACAATTTACT

upper sequence: AT2G28800.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 7
gtgagaaataaacacaagtttcttttatttttcctgttacttaaacaatttgatatgattgttctgaaaccgaatttaatttcttttgtcagACTGATGATCCTGCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCCACTCATGATCGGTTACTTTGCATTGTCTGTCCCATCAGGACTATCTATTT
|| |  |||||    |   || | | ||  ||    |  |||      |||| |    |  |  | |||  |  |||  ||| ||||| ||||||||||||||  | || |||||||| |||||||||||||||||||||||||||||||| ||||||||| |  | ||||||||||||||| |||| ||||
gtaaagaataagtcta---ttttctgatcattttcttctctt------tttgtttcattcctagtaaaattgggttt--ttttttttggcagACTGATGATCCATCTCAAAAGAATACACTTCTTGTTTTCAAGTTTCTTCCACTCATGATTGGTTACTTTTCTCTATCTGTCCCATCAGGATTATCAATTT

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|164186038|gb|ES211744.1|ES211744
EST:     TATGAAGCCTCCTCAA                         ACTGATGATCCTGCCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCC
genomic: TATGAAGCCTCCTCAAgtgagaaata ... cttttgtcagACTGATGATCCTG-CACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCC
EST: gi|124752027|gb|EH842157.1|EH842157
EST:     TACTTATTGCCTCCCAGTATGTGTCAATGGAAATTATGAAGCCTCCTCAA                         ACTGATGATCCTGCACAGAAG
genomic: TACTTATTGCCTCCCAGTATGTGTCAATGGAAATTATGAAGCCTCCTCAAgtgagaaata ... cttttgtcagACTGATGATCCTGCACAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttaaacaatttgatatgattgttctgaaaccgaatttaatttcttttgtcagACTGATGATCCTGCACAGAAGAATACGCTTCTTGTTTTCAAGTTTCTTCCACTCATGATCGGTTACTTTGCATTGTCTGTCCCATCAGGACTATCTATTT
                                    atttaat  putative branch site (score: 4)
                                          tttcttttgtc  CT-rich tract
                                   aatttaatttcttttg  TA-rich tract