Sequence
atgc intronic sequence ATGC exonic sequencegcaagtggagaaaagtggttttgtgagtggagagaagggcatgctgggcggaacggagtggcgtgagggttttcggggttgaaattatggtgcggaatggggtgggtgaggctattagagggcgagcagcagatgaattgggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
Basic information
species | Physcomitrella patens |
transcript | PP1S116_115V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S116_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 2
gcaagtggagaaaagtggttttgtgagtggagagaagggcatgctgggcggaacggagtggcgtgagggttttcggggttgaaattatggtgcggaatggggtgggtgaggctattagagggcgagcagcagatgaattgggcggagg-acgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
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----------------------------------------------------------------------------------------------gttcggtgttcttgct-ctcttgcaaaaccagttttttctttcttgtttggttttgttctaacaagttttcctccttccaacactgcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCG
upper sequence: PP1S116_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 2
gcaagtggagaaaagtggttttgtgagtggagagaagggcatgctgggcggaacggagtggcgtgagggttttcggggttgaaattatggtgcggaatggggtgggtgaggctattagagggcgagcagcagatgaattgggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
| | |||| | | || || | ||| || | | | | ||||||| ||||||||||||||||||||| | ||||| || ||||| ||| |||| || |||| ||||| ||||||| || || | || ||||| |||||||
----------------------------------------------------------------------------------------------------gttcggtgttcttgctctcttgcaagttttttctttcttgtttggttttgtctaacaaattttcctccttccaacactgcagGTTGTGGCAGTGAAGCAGCTGGATAGAAACGGACTTCAAGGAAACAGAGAATTCTTGGTGGAAGTTCTGATGCTCAGCTTGCTTCACCATCCAAATCTCG
upper sequence: PP1S116_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ14281 (Selaginella moellendorffii), 3'ss of exon 1
gcaagtggagaaaagtggttttgtgagtggagagaagggcatgctgggcggaacggagtggcgtgagggttttcggggttgaaattatggtgcggaatggggtgggtgaggctattagagggcgagcagcagatgaattgggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
| ||| || | ||| || | || ||| ||| | ||||| || || ||||||||||||||| | ||||| ||||||| || ||||||||| |||| || || || ||||||||| || | || ||||| || | |
----------------------------------------------------------------------------------------------------------------------------gtttgtggattggttttgtagagcggttttcttatacgt-ttgttgttgtgaattcagGTAGTCGCTGTGAAGCAGCTGGATAGAAACGGATTGCAAGGCAATCGAGAGTTTTTGGTCGAGGTTTTAATGCTGAGTTTGCTTCACCATCCAAACTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcagatgaattgggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
atgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtggagaaaagtggttttgtgagtggagagaagggcatgctgggcggaacggagtggcgtgagggttttcggggttgaaattatggtgcggaatggggtgggtgaggctattagagggcgagcagcagatgaattgggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAGCTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG