Sequence
atgc intronic sequence ATGC exonic sequenceAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S47_46V6.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA14G07750.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtac-tcttgactcttgaaaccattctg---gtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
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TGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGTTGCTTAATCAACTTGATGGGTTTGATCAACTTGGGAAGgtatatcttgcttcgtaaccccatttagtttgttttgaaaacccataatcacactttacttttagaaacacctgctccctttcctaacaaatttgaaggt----------------------------------------
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA04G03180.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
||| || | || || || || |||||||||||||| |||||||| | || || |||||| | | |||||||||||||| |||||||| |||||||||||| || | || || || |||| || | | ||||| | ||||| ||| | | | || ||| ||| ||| || ||| ||||
AGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGCTGCTTAATCAACTTGATGGATTTGATCAACTTGGAAAGgtatatttaattccataatcc-----------catttaacttagttaaaagcttgatccg-------ttgta---gcaaattcc---taggttaaggaatt-tttgtctttttatttttgtggag-----------
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA17G37220.1 (Glycine max), 5'ss of exon 7
-AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattgg---ctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
|| ||| | || || || || |||||||| ||||| |||||||| | ||||| |||||||| | |||||||||||||| |||||||| ||||| |||||| | || || || | || | ||| | | || | | || | || | | || | || |
GTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGTTGCTTAATCAACTTGATGGGTTTGATCAACTTGGGAAggtatatcttgcttagtaaccccacttagtttgttttgaaaaccataatcacactttacttttagaaacacctgctccctttcttaacaaatttgaaggt----------------------------------------
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA06G03230.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
||| || | || || || || |||||||||||||| |||||||| | || || |||||| | | |||||||| ||||| |||||||| |||||||||||| || | || || || | | |||| || | | || | || || | | | || | ||| | || |||
AGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatattttattccataatcccatttaac-----ttggagttaaaagcttgatccgt-tgtagcaaattccaaggttaaggaacttttgtcttctttttttttttg------------------------------
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv03s0038g04350.t01 (Vitis vinifera), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgact---cttgaaaccattctggt-attcattggctttggct-tttctgctgatctgcaagaagttgtatata--tgaat---cacgtgtgtgc-tagccgattctttatctccttgtttacatggaat-atggatgcag-----------------------------------
|| ||| | || ||||| || |||||||| ||||| || ||||| | |||||||||||||| | || || || ||||| |||||||||||||| |||||| | || | | | | |||| | || || | |||| | ||| | ||| | ||| ||| | || || || | || ||| | | || || | || | || ||| | || ||
TGGGCGTCGTTTCAGCGAGGGAACAAGTGCTGATCGTGAAATTCAGAGAACACTCATGGAGTTGCTCAACCAGCTGGATGGATTTGATCAGCTTGGGAAGgtatttttatttgtgttatcagtaactctgtttgctcttttgatttgattgtttataaccatcagtt-gaacttgcttctagttgcatgcatatatgaatgcatcaacatccctctacatgtttttgtatttggctttgtgattgtccaaaaggtgactaaatgtgaagtgtgggtttcctag
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ13668 (Selaginella moellendorffii), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
||||| ||||| || |||||||| ||||| || |||| || ||| | ||||| ||||| | || ||||| || ||||| ||||||||||||||||||||| | | ||| ||||| | ||| | ||||| | | |
CGGACGAAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgta-----gggattggaag--attctcatgttctatatagttggcctcttgtccag--------------------------------------------------------------------------------
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
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CGGACGGAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgta------gggattgaaagt-ttctcatgttctatatagttggcctcttgtccag--------------------------------------------------------------------------------Mapped 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|18338881|gb|BJ170907.1|BJ170907EST: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT