Sequence
atgc intronic sequence ATGC exonic sequence...gcttaatagataggaaaatgtttccgtttttagaagttttactgagaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S1_203V6.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S1_203V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 6
--------------------------------gcttaatagataggaaaatgtttccgtttttagaagttttactgag---aagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaac--cagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
| || | | || | | | | ||| | | || | ||| || | | ||| | ||| | ||| || || |||||||| || || ||||||||||||||||||||||| ||||| |||| |||
gtctcaagttctttctgtactaacctatgtttttatgttataaatgagatggctaacctttcttgcttttatttagagcttggtatttattatttcatcatatgacaattttttgaaaaaaaatgatgaattttcagGTTCTTGTAGCAGATATCAACATTGGTTATGAAGAAATTGTCAATATTCAG
upper sequence: PP1S1_203V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 6
gcttaatagataggaaaatgtttccgtttttagaagttttactga-gaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
| || | ||| || | | | | | | || ||| | || || || | | || | || || || || | || |||| |||||||| |||||||||||||| |||||||| ||||||| ||||||
gtatacttttggataaactgctgcattcagtgccattctttctgctgtttctcctaaggaccttatgatgtctga-ttaactctt-tgacacattaa--agGTGCTGGTGGCTGATATCAACATTGGATATGAAGATTTTGTGAACACCCAG
upper sequence: PP1S1_203V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 6
gcttaatagataggaaaatgtttccgtttttagaagttttactgagaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
|| | | ||| | |||| | | | || | |||| |||||| | ||| ||| |||||||| |||||||||||||| |||||||| ||||| || ||||||
-----gtatgctttctctcggtctttctttctgttgtttctcctaaggaccttatgatgtc------tgattaactttttgaca----cattaaa----gGTGCTGGTGGCTGATATCAACATTGGATATGAAGATATTGTTAACACCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
agctgat putative branch site (score: 4)
aacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttaatagataggaaaatgtttccgtttttagaagttttactgagaagatcggtagtgccatgagctgatgaactttacgctggtggtgccaaaaccagGTTCTGGTGGCGGATATCAACATTGGTTATGAAGACATTGTGAATACCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA