Sequence
atgc intronic sequence ATGC exonic sequence...atgttacggttaattctcacttctattttcatttagtcaagaaatgccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
Basic information
species | Physcomitrella patens |
transcript | PP1S88_199V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_199V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 9
------------atgttacggtt-aattctcacttctattttcatttagtcaagaaatgccgcctctgaacttgaaacttgcc--tgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
|| | | || ||| || || ||| | || | || | | || | | | | |||| | | | | ||| ||||||||||| |||||||||||||| ||||| |||||||| |||||| | || ||||| || || | ||||| || || ||||| | ||||||||||| |
gttctacttatcatttagcatttcaatgaacatcagtagtttttgctggtattgttttgacatttgaatacaagtatttcagcattgctaatttcattctctacttcaaac-cagCCAAGTCCGTTTTTTACGGAACAACTGACGGCTTTCGAAGTGTGGCTTGATCATGGCTCCGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTC
upper sequence: PP1S88_199V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
atgttacggttaattctcacttctat--tttcatttagtcaagaaatgccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
||| || | || ||| |||| | | | | | || || |||| | || |||| | || || |||||||||| |||||||| || || ||||||||||| ||||||||| | || ||||| || || |||||||||||||| || | || || ||||| |
--------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgt--------tttgcttataaaacg-tgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC
upper sequence: PP1S88_199V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ28980 (Selaginella moellendorffii), 3'ss of exon 9
atgttacggttaattctcacttctattttcatttagtcaagaaatgccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaatt---gcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
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------------------------------------------------------gtattgagcattatccttgtgaaaaaagctgaaaacgtgtcctgcgcagCCGAGTCCATTTTTTACGGATCAGTTGACAGCGTTCGAAGTATGGCTTGAGCACGGATCAGCGAGTAAAAGACCACCAGAGCAGCTTCCAATAGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
tttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttacggttaattctcacttctattttcatttagtcaagaaatgccgcctctgaacttgaaacttgcctgctgttcggtgtttgaaacccaattgcagCCAAGTCCATTTTTTACGGAACAGCTGACAGCTTTCGAGGTGTGGTTGGAGCATGGTTCGGAAGGGAAGAAGCCACCGGAACAACTTCCCATAGTTCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC