Sequence
atgc intronic sequence ATGC exonic sequence...aggccagtctgacacttgtaattcacgctcgtgcttcatgtccttgagattatagttgggaatgctctttcattttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S568_2V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G22550.1 (Glycine max), 3'ss of exon 3
aggccagtctgacacttgtaattcacgctcgtgcttcatgtccttgagattatagttgggaatgctctttcatt-----ttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
||| | | | |||| ||||||| ||| | | || | | | | | | | || ||| | || || | || | |||||||||||||| || | || || ||||| ||||| ||||||||||||||||||||||| | | |||| | | || || ||||| |||
--------gtgagttgctttgtctatgctc---cttcatgcttttgtagtcctcattcttagggttatcttagtgctaatttgaagcaatatacttatt--ttagGCTTGCATATTTGCATGAAGCAATTGAGCCAAAGGTGGTACACCGAGATATCAAGTCCAGCAACATATTAATTGATGACGACTTTAATGCCAAGGTTTCT
upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G28490.1 (Glycine max), 3'ss of exon 3
--aggccagtctgacacttgtaattcacgctcgtgc--ttcatgtccttgagattatagttgggaatgctctttcattttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
| | || | | | ||| ||| || | | | ||| | |||| | | |||| || | ||| | || ||| |||| | |||||||||||||| || | || || ||||| ||||| |||||||||||||| |||||||| | | |||| | | || || ||||| |||
gtgagttgctttgtctgtgctccttcgggcttttgtagtcctcattcttagggttatctt----agtgctaattta------aagcaatatacttgtt--tcagGCTTGCATATTTGCATGAAGCGATCGAGCCAAAGGTGGTACACCGAGATATCAAGTCAAGCAACATATTAATTGATGATGACTTCAATGCCAAGGTTTCT
upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv05s0020g00730.t01 (Vitis vinifera), 3'ss of exon 4
aggccagtctgacacttgtaattcacgctcgtgctt-catgtccttgagatt--atagttgggaatgctctttcattttctaagtgttttagcggttgat--cagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
| || |||| || | | || | || || | ||| || || || | ||| || | || | | ||| | | || || ||| | || || |||||||| ||| | ||||| || ||||| |||||||||||||| |||||||| || | | |||| | | || || ||| | |||
---gtaaact--cactgataccttaatctgttatttacagttgctttaggtttcatttctttcaattgtcatccacatggt--gtgatatgattttttattgcagGCTCGCCTACTTGCATGAAGCTATTGAACCAAAAGTTGTGCATCGAGATATCAAATCCAGCAATATATTGATTGATGATGAATTTAATGCTAAGATATCT
upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ31013 (Selaginella moellendorffii), 3'ss of exon 3
aggccagtctgacacttgtaattcacgctcgtgcttcatgtccttgagattatagttgggaatgctctttcattttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
| ||| ||| || | | | ||| || || || | | || | | ||| || |||| |||||||| |||||||| || ||||| || ||||| |||||||| | ||||||||||||||||| | | |||||||| ||| | |||
------------------------gtaagtttccttggtgtggacgaaag-aaaccatcaaattcttttgttttctttttaccttgcgtcttctttacagGCTGACATACTTGCATGAAGCTTTGGAGCCCAAGGTGGTTCATCGGGATATCAAAGCAAGCAACATTCTTGTGGAGGGGGACTGGAACGCGAAGATATCT
upper sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ34699 (Selaginella moellendorffii), 3'ss of exon 3
aggccagtctgacacttgtaattcacgctcgtgcttcatgtccttgagattatagttgggaatgctctttcattttctaagtgttttagcggttgat--cagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
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--------------------------gtaagt-ttccttggtgtggacgaaagaaaccatcaaactcttttgttttctttttaccttgcgtcttctttacagGCTGACATACTTGCATGAAGCTTTGGAGCCCAAGGTGGTTCATCGGGATATCAAAGCAAGCAACATTCTTGTGGAGGGGGACTGGAACGCGAAGATATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagattatagttgggaatgctctttcattttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
tttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggccagtctgacacttgtaattcacgctcgtgcttcatgtccttgagattatagttgggaatgctctttcattttctaagtgttttagcggttgatcagATTGGCATATTTGCATGAGGCTTTGGAACCGAAGGTTGTACATCGAGATATCAAGTCCAGCAACATTCTTGTGGATGCACAGTGGAACGCAAAGGTGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - -tgcttca