Sequence
atgc intronic sequence ATGC exonic sequence...catctaccaccgcatctgttttacaaaccttttctctatagaagtagaggtttccattatattttccaattgaagtccccgagtatttatctttgagcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S112_67V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 6
catctac-caccgcatctgttttacaaaccttttctctatagaagtagaggtttccattatattttcc-aattgaagt-ccccgagtatttatctttgagcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
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--tctcctcacaacctcttttttttttttgtttacttgatatata-actaattggaaatatattttcttggatgtggtataacctttattttattttgtgaagGTGATAATCACAGTATAATGATATACTATCCCAGTTCAGCTGGTGGAGGTATGAAGGAATTATTTAGGAAG
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 7
-------catctaccaccgcatctgttttacaaaccttttctctatagaagtagaggtttccattatattttccaattgaagtccccgagtatttatctttgagcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
| | | || | || | | || |||| || || | || ||| | || | | | | | | | | | ||||| ||| ||||||| | || || |||||||||||||||| || || |||||||| ||||||||||| | || || |||
ttatttttccttgctatatcagcagtgatcccaattgtttccct---gatttgcagatttttttaattgtctactaataatga----aattttttatgcttgtaaagGAGATGACCATAGTATAATGATATACTACCCTAGCTCAGCTGGTGGAGGCATGAAAGAATTGTTTCGTAAG
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 6
catctaccaccgcatctgttttacaaaccttttctctatagaagt---agaggtttccattatattttccaattgaagtccccgagtatttatctttg--agcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
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--gtgaatggcaaaagaatttt-taagccatttgttgaaaagcctgtgaatggtgcgtatagaacttcatatatacagGTTTCACTAAAGTGGCTATGCAAGCAGGAGATAATCACAGCGTCATGATCTACTATCCTAGCGCTGCTGGCGGTGGAATGAAAGAGCTTTTCCGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaggtttccattatattttccaattgaagtccccgagtatttatctttgagcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
tttatcttt CT-rich tract
attatattttccaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catctaccaccgcatctgttttacaaaccttttctctatagaagtagaggtttccattatattttccaattgaagtccccgagtatttatctttgagcagGAGATAATCACAGCGTAATGATATACTACCCAAGTTCTGCTGGTGGGGGCATGAAAGAGCTCTTCCGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT