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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G20000.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
-------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatc-tgtctctct-ctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|| || | | | | || | | | | ||| || || | | | || | | || | |||||| || ||||| || || || |||||||| ||||||||||| || || ||||| || || || |||||||||||||| ||||||||||| ||||||||||
ttcaaaacaatgtgcatatatacacagcactatagaacgtcatagctcctataccttgtgatcatgcaactttattcactttctctttcatcatcttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
-------------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|| | ||| | | | | ||| || | | || | | | || || || |||||||| || | |||||| || ||||| ||||| || |||||||| ||||||||||| || || || || || ||||| ||||| |||||||| ||||| ||||| ||||||||||
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttc--atttttttggt-gttg-gttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 8
---------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtc----tctctctaatgtttttggttattacggt--cagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
| ||| | |||| || | | ||| | | | | | | || | || | | || | | | |||||||| ||||| || || || ||||||||| | | ||| |||| ||||| ||||||||||| || ||||||||||||||||| ||||| ||||| || |
tactaatgcaaatgcagagcaatttgtttgtcaatgttaacttaatgtgttattaagtattttatagcctgaccaacgctcaaattttgtgcctttgcagGCTGTTTGCACCGAAGCTGGAATGTTTGCATTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCTGTGGCCAAGGTGATGAAAAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
----------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|| | |||| | | ||| | || | | | ||| | | || | |||| | || |||||||| ||||| || || || |||||||| | | ||| |||| ||||| ||||||||||| || ||||||||||| ||||||||||| ||||| || |
gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgcc-ttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 8
---------------gtaagtgtttc---tctgtccctgcttctgtcttgttctctccaatc---tgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
| | | || | | | ||||| |||| ||| ||| | ||| |||| |||| | ||| ||||| |||||||| || || || |||||||| || | |||||||||||||||||||| || ||||| ||||||||||| ||||| ||||| ||||| || |
actaagtccttattcttcatcatatcaagtgcggtcggttatctgttttgtcttctaacatcaagcatgtctaactaaacttttatataattgtttgcagGCGGTATGCACAGAAGCTGGAATGTTTGCTCTAAGGGAGAGGAGAGTACATGTGACACAAGAAGATTTTGAGATGGCAGTGGCAAAGGTGATGAAAAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EDO96639 (Chlamydomonas reinhardtii), 3'ss of exon 8
------------------------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTA-TGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
| | ||| | | |||| | | | | | | | | | || || | | ||||| ||||||||||||||||| || || ||| | | || || ||||| ||||| |||||||||||||| |||||
ctcacccccgcacccatgcccacttcttaaatactcatgaatgtaaccccccccctccccgccccccccccccacacacacacacacccgccctccacagCGGCGCCGAGGCCAAGGCCTGCTGCACCGAGGCGGGCATGTTTGCGCTGCGGGAGCGCCGCGTGCACGTGACGCAGGAGGACTTTGAGATGGCGGTGGCC----------------

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctc----tctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
| ||| | || | ||| | | || | | | | ||||| | |||| | || || | | ||||||||| ||||| || || ||||||||||| || ||||| || | |||||||| || || || || ||||| ||| ||||||||||||| |||||||| |
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------gtaagtgtttctctgtccctgc-ttctgtcttgttctctccaatctgtctctctctaatg-tttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
| ||| | | || || ||| | | | |||| | | || | ||||| || | | ||||||||||||||| ||||| ||||||||||| || ||||| || | ||||||||||| || || ||||| |||||||||||||| ||||| |||||||| |
gtagctacaaacctacagtatctagggtttatttctggtagtgatacgaaggaagctgctagaggcttttgtattatgttatttaaaattttggctgttcgtttatactaattttttattgcttcaatcagGCTGTATGCACAGAGGCTGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTGACACAAGAGGACTTCGAGATGGCTGTGGCTAAGGTGATGAAGAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 7
gtaagtgtttctc-tgtccctgcttctgtcttgttctctccaatct-gtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|||| | || | |||| || | || || | | || | | | | | ||||| | | | ||||| || ||||||||||| || |||||||| || || |||||| | || ||||| || |||||||| || || ||||| ||||| || || |||||||| |
------gtttgtgatgctcgcgctttagt-tggtccttgacgacggagtgtgtttttttttttttttgctctc-----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGATTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtgtttctc-tgtccctgcttctgtcttgttctctccaatct-gtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|||| | || | |||| || | || || | | || | | | | | ||||| | | | ||||| || ||||||||||| || |||||||| || || |||||| | || ||||| || ||||||||||| || ||| | ||||| || || |||||||| |
------gtttgtgatgctcgcgctttagt-tggtccttgacgacggagtgtgtttttttttttttttgctctc-----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 7
gtaagtgtttctc-tgtccctgcttctgtcttgttctctccaatct-gtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
|||| | || | |||| || | || || | | || | | | | | ||||| | | | ||||| || ||||||||||| || |||||||| || || |||||| | || ||||| || ||||||||||| || ||||| ||||| || || |||||||| |
------gtttgtgatgctcgcgctttagt-tggtccttgacgacggagtgtgtttttttttttttttgctctc-----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

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|116400365|gb|EG442957.1|EG442957
EST:     TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAG                         GCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAGgtaagtgttt ... ttacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT
EST: gi|86079899|gb|DR375656.1|DR375656
EST:     TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAG                         GCTGTATGCACGGAGGCGGGCATGTTTGM-CTTCGTGAGAGGAGAGTACAT
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAGgtaagtgttt ... ttacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
                           ctctaat  putative branch site (score: 3)
 taatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA