Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctttttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTATGATTACTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
Basic information
species | Physcomitrella patens |
transcript | PP1S9_386V6.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_386V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g01030.3 (Oryza sativa), 3'ss of exon 8
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctttttgtgtctagaccg-agttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTATGATTACTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
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---------------------------------------------------------------------------------------gtaagtgatttagaattagctaccctcattggttttcattccttgagatgacagtcactacacatgtatgtttttcc---ctcttca--acagGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG------------------------------------------
upper sequence: PP1S9_386V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctt-tttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTA-TGATTA-CTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
| | | || | ||| | | | | || ||| | || | | || || || || | | | | ||||| || ||||| || | | | || || | || || || |||||||| ||||| ||||| |||||| |||||| || |||||||| |||||||||||||||| | || | ||| | || | | | | | ||| || |
-------------------------gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaa--aaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttga------tatcaaatgttg----cttgataacatt----tctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTC--TTTTTGTATT
upper sequence: PP1S9_386V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA05G03770.1 (Glycine max), 3'ss of exon 9
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctt-tttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTATGATTACTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
| | | || | ||| | | | | || ||| | || | | || || || || | | | | ||||| || ||||| || | | | || || | || || || |||||||| ||||| ||||| |||||| |||||| || |||||||| |||||||||||||
-------------------------gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaa--aaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttga------tatcaaatgttg----cttgataacatt----tctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATG------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTATGATTACTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
ttttaat putative branch site (score: 3)
ttttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctttttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTATGATTACTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG