Sequence
atgc intronic sequence ATGC exonic sequenceATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttgtgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt...
Basic information
species | Physcomitrella patens |
transcript | PP1S378_9V6.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgta-tgttcgagattactaactcttttttgtgatccgtaacttagt----ccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt
||||| ||||||||||||| |||||| |||||||||| || | || ||||||||| | ||||| |||||||| ||||| |||||||| ||||| || |||| ||| | || || || |||| | || | | ||| | | || || | || | | ||| | || || ||| |
ATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAGgtactgtatgtcatcgctg---ctattttattttctgcagtttactattagcagcatatcaccattgcagagcatcatatctgattctaatttacgtag------
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgt------tcgagattactaactcttttttgtgatccgtaacttagtccg-gctcattgtatata-gcgaatgttttctcttgctttaggttccgttgattatt-------------------
|| |||||||| ||||||| ||| ||| |||||||||| || | || || ||||||||||||||||| ||||| ||||| || ||||| ||||| || |||||| || | | | || | | ||| || | ||| | || || | | || || | ||| || | | || |
ATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAGgtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgtacttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattacaatacag
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 5'ss of exon 13
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgtt--cgagattactaactctt----ttttgtgatccgtaacttagtccggctcattg-tatatagcgaatgttttctcttgctttaggttccgttgattatt---------------
||||| ||||||||||||||||| ||| ||||||| ||||| | || || || || || |||| | | || ||||| |||||||||||||| || ||| | | || || || | || ||| ||| | | || | | | ||| | | | || || | | | || ||| || | |||
ATTGGGGGAGCTAGTGAAGTTGAAGTTGGTGAGAAAAAAGATAGGGTAACAGACGCTTTACATGCAGCAAGGGCTGCTGTGGAGGAGGGCATTGTACCAGgtgtagtgacggttttcttattttttccactttggtgtcttttttcctaaacttgtttcttgatgttttgctttcgtgtaacttgtccatatgttttgt-gccaatttggaacttcaaacag
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 13
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttgtga--tccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttagg--ttccgttgattatt--------------------------------------------------------
||||||||||| || |||| || ||| |||||||||| || | || || |||||| ||||||| || ||||| |||||||| ||||||||||| || |||| | |||| | || | | | | || | | || | | | | || || || |||| | || || ||| |||||
ATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAGgtaatgtatcaattaaaatttcatggggggggggtgtttatgctgatttcctgtgttatttgctcctactgattcctgttgcatcagtatttgtgttagttattcctgatttcctgttgcgtcagtatgcccgggagtcaatctttaattgtgtatgcag
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttgtgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt
||||||||||| ||||||| ||| ||| |||||||||| || | || ||||||||||| ||||| || || || ||||| ||||||||||| || ||||||| | | | ||||| || || | || | || | ||| | ||||| || |||
ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTGgtaaaatatcaact-ctaacagttca--atggttagttttacaatctcaaatcagatccgactttaatttgttctcgcactgtag---------------
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttg-tgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt
||||||||||| ||||| | ||| ||| |||||||||| || | || || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||||| || | ||| | || | || ||| ||| | | ||| | | || |||| | ||||
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagatt-attagcacttgcagttgtatgctgagttctaattctacgtcgttcaat-caaatttgatgtgttgtgctttgcgcag----------------
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 12
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgt---tcgagattactaactcttttttgtgatccgtaacttagtccggctcattgtatatag-cgaatgttttctcttgctttaggttccgttgattatt
||||||||||| ||||||| ||| ||| |||||||||||||| | || || ||||| ||||||||||| ||||| || ||||| ||||| ||| | || ||||||| | | | || || ||| | | | ||| | | || | | | ||| | |||||
ATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAGgtatgtctcttccagtgaggaagactctttgatatagtgctaaaaagtttgctatgtgctaaagaaacaaatcaaaacacttgcag------------------
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 13
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 14
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatg--ttcgagattactaactcttttttgtgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt
|| |||||||||||||||| ||| ||||||||||||||||| | ||||| ||||| | ||||| || || || ||||| || || || ||||| || |||| | || | || | || || | | | ||| || | | | ||| | | || |
ATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAGgtaagctttttggtttgcattttcccttggttactactcaaccggagttggacaaatcttcataaaatttatatttgcag----------------------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|162171070|gb|FC346969.1|FC346969EST: TGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG GTGGTGGTGTTGCTCTTTTGTATGCTTCACGGGAGCTTGACAATGTTCAAA
genomic: TGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcga ... aatggatcagGTGGTGGTGTTGCTCTTTTGTATGCTTCACGGGAGCTTGACAATGTTCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTGgtatgttcgagattactaactcttttttgtgatccgtaacttagtccggctcattgtatatagcgaatgttttctcttgctttaggttccgttgattatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG