Sequence
atgc intronic sequence ATGC exonic sequence...atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttttttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11910.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttt----tttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
| || || || | | || | | | || || || || ||||| | || | | ||| |||| | | ||| || |||||||| || || ||||| |||| || ||||| ||||||||||||||||||||||| ||| ||||||| || || || ||| ||||||| |||||||||
--acttttcttcatgatcgaatc-tatgttcttgctaagttttttgatttttttttcctgaagatggtttctcaagccatatttttgaattgtgttactt-cagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
------atatttca---aagcaggaacagctgataaagttgcatttgactaatttatattgttact--ctgaact-tatcttata-----ttggaatacttttt-----ttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
| ||||| ||| | | ||| || | |||| || | || | | | |||| | | ||||| | | || | | || || | | |||||||| |||||||| || ||||| |||||||| || || |||||||| || ||| | ||| | ||||| || || |||||| | |||||||||||||||
gtactgaattttcatataagtacaatcaggtgg-atgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 8
---------atatttcaaagcaggaacagctgataaagttgcatttgactaatttat--attgttactctgaact-tatct------tatattggaatactttt----tttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
| || ||| | ||| | || ||| || | || | | | |||| | ||||| || | || ||| | || ||||||||||||||||| || ||||| |||||||| || || |||||||| || || || || ||||||||||||| || ||| | |||||||||||||||
gtgctgaatgcgctgcaccttttgaatcaaattgatgcttgaactttactgatcttctgatcatgattatgaattgtatctgtaaaccctacttcaaccaatttggggcacgtacattgcagGATGCAAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTCCAACTGAAACGGTTTGAATACGACTTCATGCGAGACACAATGGTGAAG
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 6
atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttttttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
||||| || || | | || || | || || ||| |||||||| || || || || || | || ||||| || ||||| || ||||| |||||| |||||||||| |||||| || | ||||||||||| |||
-----------------------------------------------gtttgtttttcgtgttccatgtcaagaaggtttaatggtt--gtttcttttagGATGCACGCAAGGGCGTGCTCTTTGTGGATTTTCCCCCTGTTCTCCAGCTTCAACTCAAGCGGTTTGAATATGATTTTGTGCGAGACACAATGGTTAAG
upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 6
atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttttttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
||||| || || | | || || | || || ||| |||||||| || || || || || | || ||||| || ||||| || ||||| |||||| |||||||||| |||||| || | ||||||||||| |||
-----------------------------------------------gtttgtttttcgtgttccatgtcaagaaggtttaatggtt--gttgcttttagGATGCACGCAAGGGCGTGCTCTTTGTGGATTTTCCCCCTGTTCTCCAGCTTCAACTCAAGCGGTTTGAATATGATTTTGTGCGAGACACAATGGTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattgttactctgaacttatcttatattggaatactttttttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
ctttttttattatttt CT-rich tract
aacttatcttatattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttcaaagcaggaacagctgataaagttgcatttgactaatttatattgttactctgaacttatcttatattggaatactttttttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - caaagca
- - - - - - - - - - - gataaag