Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggatattttgagattatggtatgtatctattagtaattgtgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S425_6V6.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
gtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggatattttgagattatggtatgtatctattagtaattgtgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
|| || | | ||| || || ||||| || ||| | ||| ||||| ||| ||| ||| |||| || |||||||||||||| || ||||| || ||||| || || ||||||||| | ||||||||||| |||| | |||||||||| || ||
------------------------------------------------------------------------------------------------------gt-ttgatatcttgtcatgcatatttttcctttc--------ttttaccttagcctatgttcctaaccataaaaaacctt------------tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 3'ss of exon 11
gtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggatattttgagattatggtatgtatctattagta-attg--tgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
||| || ||| | || | ||| | || || | | | | | | || || || | ||||| || ||| | ||| || | ||||||| || | |||||||| || || ||| | ||||||||||||||||||||| ||||| | |||||| | || || ||||| || || ||
-----------------------------------------------------------------------------gttagttcacactatctatacctgagtagttccttgattttctctatagcccagtgcc----ggctccgcgaatttgcagtgctt-cctattgatatgttgcctctttgattttctctactagGGTGAAGCTCTCTTTCAAACACATGAAAATTTGGAGCATTTGGCTATGATGGAGAGAGTTCTAGGTCCCCTTCCAAAACATATGATTGTCAGAGCTGA
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 8
gtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggata-ttttgagattatggtatgtatctattagtaattgtgcttgtttgcggg------tggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
| |||| ||| |||||| |||| || || ||| | | | | || | || ||| | ||||||||| || |||||||| ||||| || ||| |||||||| |||||||||||||| | || | ||||| || || ||| ||| ||||||| | ||
-------------------------------------------------------------------------------------------------------------------------gtaagtttggctctc-tggatactttttaggcaattttatccagttttgtttgtttaaatcagcttatgggcttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgagattatggtatgtatctattagtaattgtgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
tatctattagtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggatattttgagattatggtatgtatctattagtaattgtgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG