Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ34967 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 3
-------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaag-
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gtaagaaatctaattacacttctacaatcttgaaata-agtaaaggcaatgttttccttttctgtgtgtaagtgtagAATGAAGATGGAGGATGGGGTTTGCACATTGAGGGCCACAGCACCATGTTTGGCTCAGCGTTGACATATGTTTCTTTGAGATTGCTTGGGGAGGGGCCAG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 3
--------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
||| | || | ||| || || || | | ||| | | | |||| ||||||||||||||||| ||||||||||| || | ||||| ||||||||| | | ||| || ||| || | | | ||||| | | |||||
gcaaggattcagttctaaatttgtcaaccctacagtgctaacggtgatc-taattttgtcgctgcaactgtagAATGAAGATGGTGGCTGGGGCTTGCACATTGAGGGTCCAAGCACCATGTTTGGCTCAGCACTGACCTACGTTACTTTGAGATTGCTTGGAGAGGGACCAG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G821318_T01 (Zea mays), 3'ss of exon 1
--------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctgga--------agAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| || || | | || | | | | || ||| ||| | |||| |||||||| || ||||||||||||||||| || |||||||| ||| || || | | | |||||| || | || | ||||| | |||
gtaaggctattttattgataaacttgaaagttgcgtgctgggagagagcaaacttcattactctccctgaatataatgtagAATGAAGATGGAGGGTGGGGATTGCACATTGAGGGCCACAGCACCATGCTTAGCTCAGCCTTGAACTATGTTGCTTTGAGGTTGCTTGGGGAGAGCCCAA
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| | ||| | || || | ||| || | | ||| |||| ||||||||||| ||||||||||| ||||| || |||||||| |||||| | || ||| || ||| | | || | ||||| ||| | |
gtatatatattttgaacctagtcatcatcctaacctcataaatgggcttggagctt--tgaagtatgaaaatggcttatgtacatggcagAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| | ||| | || || | ||| || | | | | |||| ||||||||||| ||||||||||| ||||| || |||||||| |||||| | || |||| || ||| | | || | ||||| ||| | |
gtatatatattttgaacctagtcatcatcctaaactcataaatgggcttggagctt--tgaagtatgaaaatggcttatgtacattgcagAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTTAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0054g01480.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| | ||| | || || | ||| || | | ||| |||| ||||||||||| ||||||||||| ||||| || |||||||| |||||| | || ||| || ||| | | || | ||||| ||| | |
gtatatatattttgaacctaatcatcatcctaacctcataaatgggcttggagctt--tgaagtatgaaaatggcttatgtacatggcagAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| | || | ||| || | ||| || | | | | |||| ||||||||||| |||||||| || ||||| || |||||||| |||||| | || ||| || ||| | | || | ||||| ||| || |
gtatatatattttgaacctagtcatcctcctaacctcataaatgggtttggagctt--cgaagtatgaaaatggcttatgtacattgcagAATGAAGATGGTGGGTGGGGATTCCATATTGAGGGACACAGCACCATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCCCG
upper sequence: EFJ34967 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv09s0054g01290.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
| | ||| | | || | ||| || | | | | |||| ||||||||||| |||||||| || ||||| || |||||||| |||||| | || || || ||| | | | | ||||| ||| | ||
gtacatatattttgaacctagtcatcatcctaacctcataaatgggcttggagctt--taaagtatgaaaatggcttatgtacattgcagAATGAAGATGGTGGGTGGGGATTTCATATTGAGGGACACAGCACCATGTTTTGTACAACCCTCAACTACATTTGTATGTGCATCCTTGGAGAAGGGCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
ttttttgtctttct CT-rich tract
aattttttgtcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtaatctttctttctagcgatgttcgtgaattttttgtctttctggaagAACGAAGATGGTGGCTGGGGATTGCACATTGAAGGGCACAGCACGATGTTTGGCACTGTACTTGTTTATGTTTCTCTACGGCTACTTGGCCAAGAACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC