Sequence
atgc intronic sequence ATGC exonic sequence...tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
Basic information
species | Physcomitrella patens |
transcript | PP1S199_73V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------tgttgtcttg-atgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
| | ||| | | | || || | ||| || || ||| | | || || | | |||| | ||| | | || | ||||| ||||| |||||||| |||||||||||||| |||||||| ||| | || ||||| ||||| ||||| || ||||| ||||| ||||| ||||| |
gtgctattaaccgtctttgctttttttgaatgatctaatactttggacatcaacattttgttggcattgttatgttgtttgaga----attatcacttcagtaccatcactttgttcatttccttactcaaaccagCCGAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTC
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattc-tctggatactactt--actgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
||| || | || | | |||| |||| | | || | | || | | || ||| | | | | | || || || |||| |||| | |||||||| ||||| |||||||| ||||| || ||| | |||||||||||||| | ||||| |||||||||||| | ||||| ||||| |
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggct-aaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattc-tctggatactacttactgt--tttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
||| || | || | | |||| |||| | | || | | || | | || ||| | || | | | || || || ||||||||| | |||||||| ||||| |||||||| ||||| || ||| | |||||||||||||| | ||||| |||||||| ||| | ||||| ||||| |
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggct-aaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
tgttgtcttgatgtttctttgtttttatccatgtaatt-tttttttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
||| || | | || | ||| || ||||||| | | || | | | | | |||| | ||| | | || ||| | |||| ||| | |||||||| |||||| ||||||| ||||| || ||| |||| ||||| ||||||| |||||||||||||||||| | ||||| ||||| |
-gtttgttttgtccattattatattt--ccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttact-----ctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 9
tgttgtcttgatgtttctttgtttttatccatgtaattttttt---ttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
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----------------gtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgct--tataaaacgtgttcctatcctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
tacttac putative branch site (score: 1)
ctacttactgtttttt CT-rich tract
tgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattctctggatactacttactgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC