Sequence
atgc intronic sequence ATGC exonic sequenceACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt...
Basic information
species | Physcomitrella patens |
transcript | PP1S69_14V6.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA08G47700.1 (Glycine max), 5'ss of exon 6
ACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt
|| || || ||||| || ||||| || || ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||| || || ||||||| || | |||| | | | ||| | | | | | | || | || | | | | || ||| || |
GCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGGGACTAATCAAGgtttgtggaaatgaatcatgagatatgatacttttttcatctgtataagccgtgaacctgtatataaactggatgccgcaccttggttaaaacttaaaag
upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 5'ss of exon 6
ACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgt-gattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt-----
|| || | | || || ||||| || ||||| || ||||| || ||||| || || || ||||| |||||||| |||||||||||||||||| | ||||| | |||| || | ||| | | | ||| | | || || | | || | | || | |||| |||| | ||| |
GCTACCCCTCTTAAAACGTGGAATAGGCGTGCACCATTCTGGGTTGCTTCCCATACTGAAGGAAGTGATTGAGATACTATTTCAAGAAGGTCTCATTAAGgttgggtgctaaaacttg------tgaatccgtctgttatcatggattttggtttcatcagtgtaacaactgattgtagccttttatttttacttttctttttatt
upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ23732 (Selaginella moellendorffii), 5'ss of exon 6
ACTTCCATTACT-GAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt
| | | ||||| |||||||||||| || ||||||||||| ||| | | || ||||||||||||||||||||||| ||||||||||||| ||| | ||||| | |||||| | || | |||| ||| | | | | | |
-CCTGCCTTACTTGAAGCGCGGAATCGGAGTGCATCACTCGGGCCTGTTGCCCATTCTTAAAGAAGTTATTGAGATATTATTTCAAGAAGGGCTCGTAAAGgta--tatttgtacagcgtttc-----gtttcttcctaagttgttggatgttgcag--------------------------------------------
upper sequence: PP1S69_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ21372 (Selaginella moellendorffii), 5'ss of exon 6
ACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt
|| || | ||||||||||||| || ||||||||||| ||| | | || ||||||||||||||||||||||| ||||||||||||| ||| | ||||| | |||| | | || | |||| ||| | | | | | |
CCTGCCTTATTTGAAGCGCGGAATCGGAGTGCATCACTCGGGCCTGTTGCCCATTCTTAAAGAAGTTATTGAGATATTATTTCAAGAAGGGCTCGTAAAGgta--tatttgtgcagcgtttc-----gtttcttcctaagttgttggatgttgcag--------------------------------------------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|162156045|gb|FC332212.1|FC332212EST: CAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAG TGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAA
genomic: CAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgctt ... tggtgggcagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAGGTCTCCTCAAGgtgattgcttgtacctcattccctgaggttttttcgtttcacgaaacaaacttcggccaattccataagtagtggttgtgtttttgttttccatttacgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaac