Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
Basic information
species | Physcomitrella patens |
transcript | PP1S100_124V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttg---ttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
|| || ||| | | | || | | ||| || |||| | | | | || || | | || | | | || | | | || | | |||| |||||||| || ||||||||||||||||||||||||||||| || || ||||||||||| ||||| | | | | || || ||||||||||| |
-atgaagcattacattattgtgcta-tgctcttgttttgttcttgcttga-attacttgcatatggaaactcacatctatgtttttttgatgaactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacac-ttgttggtca--atcctattttacgaacacgtgcttttctgaat-gtattttgtt-atgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
||| || | | | | ||||| | ||||| | | ||||| | | || |||||||| | ||| | | ||| ||||||| ||||| || ||||||||||||||||||||||| ||||| || | |||||||| || |||| |||| ||||| | ||||||||||| |
-----aggattatcttaccaagccatatgcactgcatgttagattgttattaactatcctggaatttctcaatttgtttttctgatttatatgtaatccatgtagTTCGACTACCTAAAAAGTTTGGAAATAGAGGAGAAGATTAACAAGATCAAGTGGTGCCAAACAGCCAACAACGCCCTCTTTCTCTTATCTACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
---tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
||| | ||| | || | | | | || |||| || | || | | || || | ||||| || | | |||| || ||||| || ||||||||||||||||| |||||||||| || | ||||||||||| |||| ||| | | || | ||||||||||| |
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattctt---gtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctat--tttacgaacacgtgcttttctgaatgtatt-ttgttatg-cagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| | | | |||| || ||| ||||||| | | | ||| | ||||||| | || | ||||| || || || ||||||||||| || || ||||| ||||||||||| ||||||||||| || | |||| ||||| ||| || |||||||||||||| |
------------gtaatcatcatttggtcagtaatgttgcaccaac------atcctatgggtcagaagagtcaatatttataaatgtatgatcattgtttcagTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G35860.2 (Glycine max), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctatt-ttacgaacacgtgcttttctgaatgt----attttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| | | ||| | | | | || | || | ||||| || | || | || | | || | | | | ||| ||||| |||| ||||||||||||||| ||||||| || |||||||| |||||| |||| ||||| | ||| | | | || ||| | ||||| || || ||||
---acaaaactgatatttaaata-agttttctctaatcattacagtagttcaattctttcaccactactac-tattattataattattattattggtttatgtagTTTGATTACCTGAAGAGTGTGGAAATTGAAGAGAAGATTAACAAAGTAAGGTGGTGGATGTCCAACGACAGTTTGCAATTTATTCTTTCAACCAACGACA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttac-gaacacgtgcttttctgaatgtatt-ttgttatg-cagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| | | | |||| || ||| ||||||| | ||| | | || ||||||| | || | ||||| || || || |||||||||||||| || ||||| ||||||||||| ||||||||||| | | |||| ||||| || || |||||||||||||| |
------------gtaatcatcatttggtcagtaatgttgcaccaac------atcctatgggtcagaagagtcaatatttataatgtatgatcattgtttcagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatc--cagttgc--attacacttgttggtcaatcctattttacgaacacgt--gcttttctga-atgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
||||| |||| | ||| || | | | | | | | | || | ||| ||| |||| || | | ||||| || || || ||||||||||||||||| ||||| || |||||||| | ||||||||| || |||||| ||| ||| || || || |||||||| |
----------------------gtaattttcagtcactggttaatgctgcctgaaatgcttgtggagcagaaatgttaacatttatgacatgtgattgttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
tgtgtagggatactgtttgacggtaatccagttgcattacactt-gttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| ||||| || || || | | ||| | | | || || | || ||| || ||||| ||||| |||||||| ||||||||||| ||||||||||| || |||||||| |||||||| || || | |||| || | ||||| || || || ||||| |
------------gtatttgatt-tactctgttttcttcttactcagctatttggctatacctttt--atctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgc-attacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
|| | | ||| | | | | | || || | | || |||| | | | || | | | | |||||||| ||| | ||| ||||| || || || ||||||||||| ||||||||||| ||||||||||| |||||||| ||| | | |||| ||| |||||| ||||||||||| || |
-gtacattaaaacttatcaccag-atttcacttacgagtaattgtgttccttgagc-tactcaataagct--tgcttttc--aatctgttt-------cagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
-------tgtgtagggatactgtttgacggtaatccagttgcattacactt-gttggtcaatcct---attttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| | | |||| || | | | | ||||| || ||| | | | | | | | || ||| || | | | ||| | ||||| || || |||||||| ||||||||||||||||| ||||| || || |||||||||||||| | |||| ||||| |||||| || ||||| ||||| |
gtatttctttcatcagttact-cctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgct-cagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
-tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
| | || | ||| | || | | |||| | || | | | |||||| || | | || | | || | | ||||| ||||| || ||||||||||||||||||||||| ||||| || || |||||||| || || | || ||| |||||| || || || |||||||
gtatttacttttctgtgttgctaacactctaat--cattgtagttttcacggatttgtatttttttcttactaaatcta--gactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
||| | | | | | || | | || ||| | ||||| || || || ||||| || ||||| ||||| |||| |||||||| |||||||||||||| |||||||| || || | || | || | ||| | | || || |||||||
-------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacat-tactttt------gttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA
upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
||| | | | | | || | | || ||| | ||||| | | || || ||||| || ||||| ||||| |||| |||||||| |||||||||||||| |||||||| || || | || | || | ||| | | || || |||||||
-------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacat-tacttttttt----ttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACAMapped 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|162182433|gb|FC358032.1|FC358032EST: GACATCTAGAGTATCGTTACTCCACTGAGTTTCAAAGTCATGAGCCAGAG TTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGA
genomic: GACATCTAGAGTATCGTTACTCCACTGAGTTTCAAAGTCATGAGCCAGAGgtattgcaaa ... tgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
ttttgtt CT-rich tract
aatgtattttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgtgc