Sequence
atgc intronic sequence ATGC exonic sequencegtacaaagtttatttcttctcctcgattcgcgattcgcttgagttgagttcttttaaaactggatgctggacttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14885 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os04g04240.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtac---aaagtttatttcttctcctcga-----ttcgcgattc---gcttgagt-tgagttcttttaaaa-ctgg---atgctggacttttgttcc------agGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
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gtaagtacctgttacggactaaaacggtacttagaaatttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
upper sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os04g04254.2 (Oryza sativa), 3'ss of exon 12
----------gtacaaagtttatttcttctcctcgattcgcg-attcgcttgagttgagttcttttaaaactggatgctggacttttgttcc------agGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
| | | || | | | || || | || | | ||| | | || | | |||| || | |||| ||||| || || |||||||||||||||||||| |||||||| |||
ttatctaatttgattgaaagaacttatgatgttaagtttgcatgtgcgttcagggagaggctagctcactctttgtttttttttttttttacttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
upper sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G021849_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------------------------gtacaaagtttatttcttctcctcgattcgcgattcgcttgagttgagttcttttaaaactggatgctggacttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
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gtaagccattccttgaaacgtctctcttttagcatattatctgacctttacaatgtgtgcgtgcgtgcgcacctgcgtggagagagagtggctacaagtttacatgaaatacttatgggtgaatttatgctgcttgttaagacagttgtgcttacactttcattttttctgcctccatagGTGCATCATGGTGGCGCTGGAACAACAGCCGCAGGTCTCAAAGCAGCG
upper sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA18G28130.1 (Glycine max), 3'ss of exon 11
------gtacaaagtttatt--tcttctcctcgattcgcgattcgcttgagttgagttcttttaaaactggatgctgga---------cttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
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agaaaaatccaggttacatgaatatactcatcaatgaaaatccagtgtgaattatctatttgcaaatttttgttcttatagctttatccatttgttgcagGTTCATCACGGAGGTGCTGGCACAACAGCTGCGGGGCTCAAAGCTGCT
upper sequence: EFJ38334 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv07s0005g05600.t01 (Vitis vinifera), 3'ss of exon 11
----------------gtacaaagtttatttcttctcctcgattcgcgattcgcttgagtt----gagttcttttaaaactggatgctggacttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
|| | | | || || || | | ||| || | || | | ||| | ||| | || | |||| || ||||| |||||||| |||||||||||||||||||||||||| ||||| ||
ttttgaatgtttctgagttctga-cacactttttgtctaagtactgtttttcctttcaattctcaagggttagttatcattggtt--tgcaattttctttcagGTACATCACGGGGGAGCTGGAACAACAGCTGCTGGTCTTAAAGCTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcgattcgcttgagttgagttcttttaaaactggatgctggacttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
cttttgttcc CT-rich tract
ttcttttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaagtttatttcttctcctcgattcgcgattcgcttgagttgagttcttttaaaactggatgctggacttttgttccagGTTCATCACGGTGGAGCTGGAACAACAGCTGCTGGTCTCAAAGCCGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT