Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
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-----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGGMapped 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|EG442957EST: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAG GCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAGgtaagtgttt ... ttacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT
EST:
gi|86079899|gb|DR375656.1|DR375656EST: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAG GCTGTATGCACGGAGGCGGGCATGTTTGM-CTTCGTGAGAGGAGAGTACAT
genomic: TGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTGCTGAGCTGAAGgtaagtgttt ... ttacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACAT
atgc intronic sequence ATGC exonic sequenceIntronic 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