Sequence
atgc intronic sequence ATGC exonic sequence...gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
Basic information
species | Physcomitrella patens |
transcript | PP1S70_177V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g33910.2 (Oryza sativa), 3'ss of exon 1
---------------gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaa----cgtttttatgaaatgcacaatg-gaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
|| || | | | || | | ||| | | |||| || | | || ||| ||||||| || | | | ||||||| | |||||||| || || |||||||| ||||| ||||| ||| | ||||| || || || ||||| |||||||||||||||| || || ||||
gtgagatcgcattgaccatggacaccatcgtctcctccttcttgattctgttc-tattctgaatctctgacgcgttcgttggatttggggattcgtttttgctcgttgtgggacgagcagGTGGCGATCGCGCACACCATCGGGCACGTGGCGGCGACGGTGAGCATGGCGAAGGTGGCGGTGTCGTTCACCCACATCATCAAGAGCGGCGAGCCGGCGT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtaca-ctgggatgtattctaacgtttttatgaaatg-cacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | | || | | | | || || | ||| | | || | | | | | | ||| | | | | |||| || | ||||||||||| || |||||||| ||||| ||||| ||| ||||||| || || || |||||||||||||||||||||| || || || |
--gtgagtatcatcggcgccgattaattcctccctaaagatctcttcttctagatgcggctctgtctcggtgtggtgctgatgcgaatcgtctcgttctcagGTTGCGATCGCGCACACGATCGGGCACGTGGCGGCGACGGTGAGCATGGCCAAGGTGGCCGTGTCGTTCACGCACATCATCAAGAGCGGGGAGCCGGCAT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1
---gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || | | || || | | | | || ||| | | | | | | ||| || | | | |||| || || || || ||||| || || ||||| || |||||||||||||| || ||||| || || || |||||||||||||| |||||||| || |
ggcaaaatagtaaagagattagggggtaaaagaaatcataatcgtcaagcattaatgtcaattagtactcaatggggaatttg---aaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1
-------gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || | ||||| ||| | || || | | | || | | | | | | | | ||| | ||| | |||| || |||| ||||| ||||| || || || || |||||||| ||||||||||| || || || ||||| |||||||||||||| | ||| || || |
aagtaacgcgtttatggtggtcaaatggtg--ggtgagtttga-agtaaggaa-aggttgatttagtagtactcactaaagaaatttca---aatttttttgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1
-----gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| |||| || | |||||| || | || || | | | || | | | | | | | | ||| | || | | || | ||| || |||| ||||| ||||| || || || || |||||||| ||||||||||| || || || ||||| |||||||||||||| | ||| || || |
gcaatgcatttatggtggtcaaatggtgtgagtgagtttga-agtaaggaa-aggttgattgagtagtactcacttgagaaatttca--aattttattgtgca-gGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1
---gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | | | | || || | | | | || | | | | | |||| | ||| || | | | |||| || || || || ||||| || || ||||| || |||||||||||||| || ||||| || || || |||||||||||||| ||||| || || |
tacaaaatagtgaagagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaatttg---aaattttgggagtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactggga---tgtattctaac----gtttttatgaaatgc-acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
|| ||| || | | | | | || || | | | | || | ||| || | | ||| | | | | ||||| || | || |||||||| |||||||| ||||| || ||||||||||| || || ||||| |||||||| |||||||| || || | ||||| || |
--------ttcatgatgttgttgcttgatggatttataattttgtttgttgtctgataatgaaagagtgtgttttgatcgatgttcccgttttttcttattcttcaagGTCGCTGTAGCACACACGATAGGACACGTTGCAGCAACAGTGAGTATGTCAAAAGTAGCAGTTTCCTTCACACACATCATTAAAAGTGGTGAACCAGCTT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttgcaatgtgggat-tggtgttggtaacactggca-gcactgcttatctttgt-acactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | || | | | | || || | | || | | | | | |||| | | | | | |||| | || |||||| || | ||| || |||| ||||| ||||| || ||||| || || ||||||||||| ||||| || || || ||||| |||||||||||||| | ||||| ||||
cttgtcattatatagcttctagtatt--tcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatata-gGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15098 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcact-gcttat-ctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || ||| || ||| | | | || || | | | ||| | | | |||| || ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||| ||||||||| | ||||| || |
----------------------------------gtaagctctcgctcatgcttggctaaacgagaaata----acaatctctattgtgttctcctgtacagGTAGCCTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ15095 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || ||| || ||| ||| ||| ||| | ||||||| |||| || || ||||| ||||| || || || ||||| ||||||||||| || || |||||||| || |||||||||||||| || || || |
--------------------------------------------gtaagtcctccac-ctgcga---gctcttgactttccgctaaaaccacga--acagGTGGCGCTGGCTCATACCATTGGGCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCATATCATCAAGAGCGCGGAGCCAGCCT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37591 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcact-gcttat-ctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| ||| || ||| || ||| | | | || || | | | ||| ||| | |||| || ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||| ||||||||| | ||||| || |
----------------------------------gtaagctctcgctcatgcttagctaaacgagaaata----acaatctctattgtgtgctcctgtacagGTAGCTTTGGCCCATACCATTGGTCACGTAGCAGCGACGGTGAGCATGTCCAAGGTGGCTGTCTCCTTCACGCACATTATCAAGAGCTCGGAACCGGCAT
upper sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37594 (Selaginella moellendorffii), 3'ss of exon 1
gtatttgcaatgtgggattggtgttggtaacactggcagcactgcttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
| | | || ||| || ||| ||| ||| ||| | |||| || |||| || || ||||| ||||| || || || ||||| ||||||||||| || || |||||||| ||||||||||||||||| || || || |
--------------------------------------------gtaagtcctccac-ctgcga---gctcttgactttccgctaaaaccacga--acagGTTGCGCTGGCTCATACCATTGGTCACGTTGCCGCCACGGTGAGCATGTCCAAGGTTGCCGTCTCCTTCACTCACATCATCAAGAGCGCGGAGCCAGCCTMapped 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|208355127|gb|DC926750.1|DC926750EST: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCG GTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
EST:
gi|67726624|gb|BJ976883.1|BJ976883EST: TCGTGCCGGCACCAGACGTAGACGCNGAGTTCTGGAAGGGACTTTTTCCG GTGGCATTGGCGCACACGATTNGGACACGTGGCAGCGACTGTGAGTATGTC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATT-GGACACGTGGCAGCGACTGTGAGTATGTC
EST:
gi|162196937|gb|FC375188.1|FC375188EST: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCG GTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
genomic: TCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
27 (upstream exon),
35 (downstream exon)
Score:
15GTCCCTTGCCGCGGGTTCAGCGATCATGCTGATTTCATGGGCCCTGCGGATCGTGCCGGCACCAGACGTAGACGCGGAGTTCTGGAAGGGACTTTTTCCGgtacgccact ... acaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctttgtacactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT
ttctaac putative branch site (score: 15)
tttttatgaaat TA-rich tract