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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttttacgactctttttgttttgttgccatggtgattttagttagttactaaaactttttgtaaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA

Basic information

species Arabidopsis thaliana
transcript AT1G27400.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G27940.1 (Glycine max), 3'ss of exon 4
gttggttttacg-actctttttgttttgttgc-catggtgattttagttagttactaa--aactttttgtaaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
    || |||   ||||||||| |  | || |  ||||  |||||| | | || | ||  || |   || |||   |||  || |||||| |||||||||||||| ||||| |||| ||||||||| |||||||| || ||||||   || || ||  |  | ||||| || || |||||||||||||
----gtattatatactctttttttccttttccatatggctatttta-tgatttccaaactaattaactgaaaattgtttcttt-tcagGTGAAAGGTTTGGATGTTGATGCGCTTTACATTTCTCATATCCAAGTCAATCAAGCACAGAAGCAAAGACGCCGAACATACCGAGCCCATGGAAGAATCA

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G01110.1 (Glycine max), 3'ss of exon 4
-----gttggttttacgactctttttgttttgttgccatggtgattttagttagttactaaaactttttgtaaacc--atttggttat----cagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
         || | |  | |   |||| ||| |    ||| | ||||||  |      | ||| |  || ||       ||| | | |    ||||| |||||||||||||||||||| || | ||||||||| ||||| || || ||||||   || || ||  |  | || ||  | ||||||||||||||||
gtatgtcctgtataagcatttgatttgatttttcat-atgattattttaagtcaactttcaaagtcattatacttttggttttgctttgccacagGTGAAAGGTTTGGATGTCGATGCTCTGTACATTTCTCATATCCAGGTTAATCAAGCACAGAAGCAAAGACGCCGCACCTACAGAGCTCATGGAAGAATCA

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G10910.2 (Glycine max), 3'ss of exon 4
gt-tggttttacg-actctttttgttttgttgccatggtgatttta-gtta---gttactaaaactttttgt---aaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
|| ||  | ||   ||| |||||   || |    ||||  |||| | |  |   ||| | |||    |||     |||   |||  || |||||| |||||||||||||| ||||| || | |||||| || |||||||| || ||||||   || || ||  |  | ||||| || || |||||||||||||
gtatgtctatatatacttttttttgcttttccatatggctatttcatgccaactgtttccaaattaatttaactgaaatttttttcttttcagGTGAAAGGTTTGGATGTTGATGCACTGTACATTTCGCATATCCAAGTCAATCAAGCACAGAAGCAAAGACGCCGAACATACCGAGCCCATGGAAGAATCA

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 3'ss of exon 3
gttggttttacgactctttttgttttgttgccatggtgattttagttagttactaaaactttttgtaaaccatttggttat-cagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
||  || ||      |  ||     |||    ||  |    || ||   | | |  ||||   |   ||   |    |  | ||| | |||||| ||||||| ||| | || | ||| |||||||||||||||||||| |||   ||||| ||| |  | ||||| || ||||||||||||||||
gtatgtattcaattgcccttcaccatgt----attctctgctttgtctataattccaactaactaataaatgtcaattcttacagTTGAAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGGGCTCATGGAAGAATCA

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g03370.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gttggttttacgactctttttgttttgttgccatggtgattttagttagttactaaaactttttgtaaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
                         ||  ||  || || | ||| |          || |   |    ||| ||| |     |  |  ||||         |  ||| | |||||| ||||||| ||| | || | ||| |||||||||||||||||||| |||   ||||| ||| |  | ||||| |||||||||||||||||||
gtatgtatttcgttgcccttcaccatgtattctcggctttatttatagc-cccttttgatagatagctttatttattgcccttactaataaatgtcaattcttacagTTGAAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGTGCTCATGGAAGAATCA

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|164007937|gb|ES013719.1|ES013719
EST:     CGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
genomic: CGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
EST: gi|124866744|gb|EH951181.1|EH951181
EST:     CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCG
genomic: CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCG
EST: gi|47827860|gb|CK117544.1|CK117544
EST:     CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
genomic: CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
EST: gi|125263279|gb|EL277364.1|EL277364
EST:     CTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTG
genomic: CTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTG
EST: gi|86074318|gb|DR370075.1|DR370075
EST:     CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
genomic: CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
EST: gi|164059501|gb|ES033960.1|ES033960
EST:     CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATG
genomic: CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATG
EST: gi|116444090|gb|EG486682.1|EG486682
EST:     CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAG                         GTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC
genomic: CTGCTCAATTCGTTCTTGATCTTCTCAAGAATGCTGAGAGCAATGCTGAGgttggtttta ... tggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatggtgattttagttagttactaaaactttttgtaaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA
                     tactaaa  putative branch site (score: 1)
                        taaaactttttgtaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttttacgactctttttgttttgttgccatggtgattttagttagttactaaaactttttgtaaaccatttggttatcagGTCAAAGGTTTGGATGTCGATGCCCTTTTCATTTCTCACATCCAAGTGAACCAAGCAGCAAAACAGAGGAGAAGGACATATCGTGCTCATGGAAGAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA