Sequence
atgc intronic sequence ATGC exonic sequence...aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ26861 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
---------aatgcgcagtttacctgggtgagtgtcactctttgt-tgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcg--cagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | | | | ||| | || | ||||| | | | | | | | | || | | || | | || | | ||| || ||||||| || |||||||| ||| |||||||||| ||||||||||||||||||||||| ||| | || ||||||||| ||
gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcg-tggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------------aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | | | | | | | | | | || | | | ||| | | | | ||| || || | || | |||||||||||| | ||||| ||||| ||| |||| |||||||| ||||| ||||||||||||||||| | || ||| |||||||||
gtaaggtttcttaagaccttaatatctttttattttcttttaattcaggttgaaattctcagagcttagattaaccagacagttaaagatagatatcaattaatataaatgcttatgatgt-taacaaaagaggaaaattgatgtttattcaag---tcatttcgaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCGAGAGCTTATGATCTAGCGGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA14G10130.1 (Glycine max), 3'ss of exon 6
aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgctt----gaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | | | || | | || || || | ||| | | | || | | | ||| ||| ||| | |||| | ||| |||||||||| ||||||||||| || | || |||||||| ||||| |||||||||||||||||| | || ||| ||||| |
gctacaagtccttttccaaagggtctgcattttcaatgctcatacttttacagaatactaatttgatgaggggtgaattttttttgtttg---tgaac-tgaagGTGGTTATGACATGGAAGAGAAAGCCGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACGCACATAAACTTCTCG
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------aatgcgcagtttacctg--ggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtt--------tcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | || || || | | | | | || | || | | ||| | | | | | |||| | || | | | | |||||||||||| | ||||| |||||||| |||| |||||| |||| || ||||||||||||||||| | | || || || ||
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaat-------gtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | ||| || ||| | | || || || | ||| ||||| | | || |||| || | || || | |||| | ||| |||||||| | ||||||||||| || | || |||||||| ||||| |||||||||||||||||| | || ||| ||||| ||
tactagttcttttccaaagtgtccgcg--ttttcagtgctcatactt----tttttactaaatgctaatttgattagtggtgattttttttgtttgtgaac-tgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
-----aatgcgcagtttacctgggtgagtgtcactctt-tgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
| | | | | | | | | ||| || || || | || ||| ||| || || | || | |||||||||||| | ||||| ||||| || |||| |||||||| || || ||||||||||||||||| | || ||| |||||||||
cagacagttaaagatagatatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgttt---attcaag---tcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 4
--aatgcgcagtttacctgggtgagtgtcactct-ttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
|| | |||| | | | | | | || | || ||| | | | | || | || | | | |||||||||||| | ||||| ||||| || |||| |||||| |||| || ||||||||||||||||| | || || || || |||
ttaacttgaagttaaagatatcatttaatattttgctcatgatgatggcaaaagaagaaatataaatgctaatacaagtgatt--ccaaaattttac-tatagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCCCATATAAATTTCCCT
upper sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
aatgcgcagtttacctgggtgagtgtcactcttt-gttgttcg-tgcttgaagttttttttcgttcc-tcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
||||||| || ||| || | | | | |||| || | | | ||| | || | | || || | ||| |||||||||||||| ||||| ||||| || |||| ||||||||||| || || ||||||||||||||| | ||| ||||| || ||
---tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
atttaat putative branch site (score: 4)
atttaatgtttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
- - - - -tttacct
- - - - - - - - - - - - - - -tctttgt
- - - - - - - - - - - - - - - - - - tgttcgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctt