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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaatagtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 15
gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaatagtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
       || |  ||         ||  |||    ||  |  |  ||  ||  ||||    |  | | |||||| ||  |  | |    | |||| |  ||    ||||||| ||||| ||||| ||||||||||||||||| ||   ||| || || |    ||||||||| || || ||||||||||| || || || || || ||||
-------cttttgtggaaaaactcaattctgtcattgtgttccattt--tctagaaacccttcaggatatagtatcacctaatgtgatgtttctt-tcatgacgctgcagCTAAGGAAGATGCTTGATCTTCTGGTACATGCCTCGACATGCCGCTCTGGCAGTTGTCAATACCCAAACTGCCGGAAAGTCAAGGGACTGTTTCGTCATG

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 17
gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaata-gtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
        | |  ||  | ||  || | |  |   |||||   |   | |  || |  || | |||| | |  ||  || | |  | |       | || |  ||   |||||  |||||||||| ||||| || || |||||||| ||||||||||| |||||||| |||||||| ||||| || || ||||| ||||| ||||| ||||
-----tgtttttttggccattcttacacc--accttgcttgg-tggggatattgcacctt-tctgcatacatataggatctctgatataaatgaattttataatt--acagCTACGGAAAATGCTTGATCTCCTTGTTCATGCATCCCAATGTCGTTCTGCACATTGCCAATATCCCAATTGTCGCAAGGTGAAGGGGCTTTTCCGCCATG

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 15
gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaatagtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
  ||    | |     | ||| |   | ||      |    | | |||  |||    | || || || |||| |     | | |  | |       || |    || |||||  |||||||||| ||||| || || |||||||| ||||||||||| |||||||| |||||||| ||||| || || ||||| || || ||||| ||||
--atgttttttggccattcttacaccaccttgcttggtggttatattgcacctt---tctgcatacatatagga-----tctctgatataaatgaattgtataattacagCTACGGAAAATGCTTGATCTCCTTGTTCATGCATCCCAATGTCGTTCTGCACATTGCCAATATCCCAATTGTCGCAAGGTGAAGGGACTTTTCCGCCATG

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 15
gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaatagtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
   |  ||| | |  |  | || ||  || |||    |  |   ||| ||  ||| |||    | | |    |||  | |  | ||  |    ||  |     ||| ||| |  | |||||||| |||||||| || |||||||| ||||||||||| || || || |||||||| ||||| || || ||||| ||||| ||||| ||||
---ttgacttt-caatctcattttatcaccgatt---caccatgcttagtggtgatattgcacttctatctataaggtctgatgttaatggattttat---aatttacagTTACGAAAAATGCTTGATCTTCTTGTGCATGCATCTCAATGTCGTTCTGCCCACTGCCAATATCCAAATTGTCGCAAGGTGAAGGGGCTTTTCCGTCATG

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 14
---gtatacactatactgttcctttctaaaactgatggtgcttctctcttggtcctgaaatttgtatgcaaatag-taacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
   | |   |  ||   |   ||| ||    |||    ||| | | |     |  |   || | | | ||||    | ||||| |||  || ||         ||    ||||||| || |||||||| ||||| ||||| |||||||| ||||| |||||  |||||||||||||||| || || || |||||||| || || ||||| ||||
agagaaatgaacatgggggatcttgct----ctgtgcatgcat-tattggaatattatcatctttctacaaaggcctgacattatttggttatt---------tgacactgcagCTAAGAAAAATGCTTGATCTACTGGTGCATGCATCTCAATGCCGTTCTCCACATTGTCAATATCCAAACTGTCGCAAAGTGAAGGGCCTTTTCCGCCATG

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|124883697|gb|EH962599.1|EH962599
EST:     CAAAACAAAGAAGCGAGGCAATTGCGAGTCTTGCAG                         CTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCA
genomic: CAAAACAAAGAAGCGAGGCAATTGCGAGTCTTGCAGgtatacacta ... ggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgtatgcaaatagtaacattttttttttgttctcttcttttggttttgcagCTTAGGAAAATGCTCGATCTTCTGGTACATGCATCACAATGTCGTTCGGCACATTGTCAATATCCGAATTGCCGGAAAGTGAAAGGGCTATTCCGACATG
              tagtaac  putative branch site (score: 1)
                    cattttttttttgttc  CT-rich tract
           aaatagtaacattttt  TA-rich tract