Sequence
atgc intronic sequence ATGC exonic sequence...gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
Basic information
species | Physcomitrella patens |
transcript | PP1S2_60V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 2
-gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
|||| ||| | | | || | | || | | | || |||| || || | | | || | || || ||||| || || || | || || || | | |||||||||||||| || |||||||||||||| ||| |||||||| || | || | || ||
tgatactgactgctgctagctagatagctagctcaatcctgct-agctgtttgatattctaatttctaagtaagctgttgctgtcatgatcaaacctgcagGTGGTCAGCCATTGCCAAGCACCTCCCAGGTAGGACTGACAACGAGATCAAGAACTACTGGAACACACACCTGAAGAAGGATCTGATCCAGAAGGGCATC
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
-gatatagacca-agacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
||| ||| ||| || ||| ||| | || | || | | | | | | | || ||||| || || || | || || || || || ||||||||||| || |||||||||||||| ||| |||||||||| ||| || || ||
ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgc--aggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G05100.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
||| ||| | ||| || | ||| || | ||| | | | || || || | || || |||||| | || ||| | | ||| |||||||| || || || | | || | | || ||||||||||| |||||||| |||||||||||| | | || ||||| || | || |||||
gtgagtttgaacttttcaataattttatatttttgccattacgtagtttatacgaaaactactaatcttgtagat-tagtcttagagtcatagc-tttgaatgatgttactagtgatttatgttaaatctacaatg-catcagattctaact--ttgtttgctttcgtatagGTGGTCTGCGATTGCGGCTCGTTTGCCTGGAAGAACAGACAACGAGATCAAAAACTATTGGAACACTCACATCAGAAAAAGACTTCTAAAGATGGGAATC
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18722 (Selaginella moellendorffii), 3'ss of exon 1
gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataatt-cttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
| | || || | | ||||| | | | ||||| | || | | | || | || | ||| | || ||| || |||| | || | ||||||||||||||||||| |||||||||| ||| | ||||||
-------------------------gtgaaaccggtaacagtttgtagagttttacctctaaattctgcgttctctaagttcttgcgtgtttcactttcagGTTGTCCGTGATCGCATCGCACATTCCTGGACGAATTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAG---------------------
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18565 (Selaginella moellendorffii), 3'ss of exon 1
gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatt-tctaaataatt-cttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
|| || | | ||||| | | | | || ||||| || | | | || | || ||||| | || ||| || |||| | || ||||||||| |||||||||||||||||||||| ||| | |||||| | | ||||||| |||||
----------------------------------gtaacagtttgtagagttttacctctaaattcttgcgttctctaagctcttgcgtgtttcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACAAGATTAAAAACTACTGGAACACACACCTCAAGAAGCAATTGTTGCAAATGGGAATC
upper sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 2
gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataatt-cttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
| | ||| | || | ||||| | || | |||| || | || ||||| | || ||| || |||| | || ||||||||||||||||||||| |||||||||| ||| | |||||| | | | || || || |||
--------------------------------------------------gtaagagtttgtagagttttacctctaagttcttgcgtttctcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAGCAATTGTTACAGATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
ttctaaa putative branch site (score: 2)
ttcttttccc putative PPT
tattcatttctaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatatagaccaagacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA