Sequence
atgc intronic sequence ATGC exonic sequence...ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
Basic information
species | Physcomitrella patens |
transcript | PP1S88_36V6.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
ttttctggctttcaaaagacgatattttcttttactgcccc-acgtgttgctgccaagtagtgggtttcatgatgagt-tcttttttgct-taatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
| | |||| | | | | || | || | | | || | ||| | | | | | | |||| || | | |||||| || ||||| || |||||||||||||| |||||||||||||| ||||||| |||||| ||||| || || | |
-gtaattccttttagct--ccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os03g62640.3 (Oryza sativa), 3'ss of exon 9
ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgcc-aagtagtgggtttcatgatgagt-tcttttttgct-taatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA------------------
| | |||| | | | | || | || | || | || | ||| | | | | | | |||| || | | |||||| || ||||| || |||||||||||||| |||||||||||||| ||||||| |||||| ||||| || || | |
-gtaattccttttagct--ccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGGTACATTCTTGCATACCC
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G028096_T04 (Zea mays), 3'ss of exon 10
---------------------------ttttctggctttcaaaagacgatatttt---ctttta----ctgccccacgtgttgctgc-caagtagt---gggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
| | | | || || | ||| |||| | | | | ||| | |||| |||| ||| ||| | ||||||||||||| |||| || |||||||||||||| || ||| ||||||| |||| || || |||| | ||| |||
gtgcgtgtttattatacatgtacatgtactattatcatgtgaaggatagtttttaaggctttaataacttatcataaactttgttatatgtatagttcacagtttaccagcatagctaatttcccttttgatccacagTGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G028096_T02 (Zea mays), 3'ss of exon 9
------------ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
|||| |||||| | || || |||| | | || | | | || | | | | | ||| ||||| | | ||||||||||||| |||| || |||||||||||||| || ||| ||||||| |||| || || |||| | ||| |||
gtgaaggatagtttttaaggctttaataacttatcataaacttt----gttatatgtatagttcacagtttaccagcatagc--taatttcccttttgatcca------cagTGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttt----tttgct-taatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
|| || | | | ||| | || | | | ||| |||| || || ||| | | | | || | || | | || ||||| ||||| | || || ||||||||||||||||| || ||||||||||||| ||| || || || | | || | |
----gtgcctgttagagataaataatggaactttaaactatatct-ttgtcaccaatctgttatttgcatttggcaatgtcaaaaatctgttgtactgcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG
upper sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
------ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
|| | |||| || | | |||| | || | | | | || | | || || ||| |||| | || ||||||||||||||| | || || ||||||||||| ||||| |||||||| || ||||| || || || ||||| | || | |
agaaaattatggggctaccata---ctatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgat---ttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208356042|gb|DC957286.1|DC957286EST: AAGTTAAGAGTGTGTGATATTTGCGGGGCATTTTTGAGCATCTATGACAG TGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACAT
genomic: AAGTTAAGAGTGTGTGATATTTGCGGGGCATTTTTGAGCATCTATGACAGgttcgtactg ... atactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACAT
EST:
gi|162204260|gb|FC379733.1|FC379733EST: AAGTTAAGAGTGTGTGATATTTGCGGGGCATTTTTGAGCATCTATGACAG TGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACAT
genomic: AAGTTAAGAGTGTGTGATATTTGCGGGGCATTTTTGAGCATCTATGACAGgttcgtactg ... atactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
gcttaat putative branch site (score: 4)
tactttc CT-rich tract
ttttttgcttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC