Sequence
atgc intronic sequence ATGC exonic sequencegttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
Basic information
species | Physcomitrella patens |
transcript | PP1S8_312V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcc-tctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgtt--gcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|| | | ||| | | || ||| | || ||||| | || |||| | | ||| || || | || | ||| ||| |||| || || | || ||||||||| | || ||||| || ||||||||||||||||| || ||||| ||||| |||||||| || | ||||||||||| ||
----------------------------------agtttcttgtagaacactaaaaggagtccttgcttagtt---atgct-ttatgcctgat-gttttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|| || | | | || | | | || ||| | || | | ||| |||||| ||| | || || | || || |||| || || | || || || | | | || ||||||||||||||||| |||||||| || || || || || ||||||||||| | ||||| ||||||||
----------------------------ttgctttg-gtcatttgga-ctgctatatgtattttatggaccttaagttc-atcaccaatgatctcat-tgtaaacaaaatctt----atatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgc-tgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|| | | | | ||||| | | | ||| | | || | | | ||| | || | | | || || ||| | |||| || || | || || || ||| | |||||||| ||||| |||||||||||||| ||||| || || || ||||||||||| | |||||||| || ||
------------------------------------tgatatgggtgcctctttcagtttgtc-agctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
| | | | | || | ||||| ||| | | | | | || |||| | || | | | | | || | || | | | ||| | ||||||| ||||| || || || || ||||| ||||||||||| |||||||||||||||||||| ||||||||| | ||||| || || | ||||| || |||||
-------------------tatatttgcccttaaaatgattaatgaa-ttgtttgaccgtgt---gctgcttgaga---------gttttaacactgattttgataatatatttct----tttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcat--acttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
||| || | | || | | || | | || | ||| |||| | | || | || ||| || ||| ||||||| ||||| || || || || || || ||||||||||| |||||||||||||||||||| ||||||||| | ||||| || || | ||||| || |||||
-------------------------------------atcatattttcccttataatgattaataaatttgtttggc-ctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttg-aaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|| ||| || || | | | | || ||| | || |||| || | || | || | |||| |||| ||| ||||| | || ||||| || || |||||||| |||||||| ||||||||||||||||| || || || ||||| || || | | || ||||| ||
-----------------------------------gtaatgttcaggcaca---cagatttaatagttattgatgaatcccattgcctatgctcatttttttt----ttttttttttaatgtgaattcc------agGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|||| || | | ||| | |||| | | ||| ||| |||| || ||| || | || || || | | || ||| || |||| |||||||||| | || |||||||| || || ||||||||||||||||||||||||||||| || |||||||| ||||||||||| | |||||||| |||||
----------tttccattggtagctt--ttttttggtg----aagcaacatttttccaagttttgtatattt--------attcaaaattattttctaaaccaatgtgatcatggaa----tgtt--------cagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG
upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
|||| || ||| ||| ||| | ||| || | ||| | | | | |||| ||| | || | | | || | || | || | ||||||||||| | || ||||||||||| |||||||| |||||||| |||||||||||||| || |||||||| ||||| ||||| | || || || || ||
---------------cctgaagct----tttagtggtcttgtctatcacctttgtgttacctt--gttatggaaggtgctga-------gatgatgttctccaac----taatatgattgtgggttttt----cagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGMapped 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|100398889|gb|BY990566.1|BY990566EST: CAACACCTCANACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAG GTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGA
genomic: CAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttct ... cctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGA
EST:
gi|162149955|gb|FC326278.1|FC326278EST: CAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAG GTATCACTTTGGCAGAATACTTCACGGATATGGGTTACAATGTCAGTATGA
genomic: CAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttct ... cctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGA
EST:
gi|162154257|gb|FC330388.1|FC330388EST: CAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAG GTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGA
genomic: CAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttct ... cctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGA
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:
18 (upstream exon),
18 (downstream exon)
Score:
1TTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttct ... cctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
ctgtttcct CT-rich tract
atcattat TA-rich tract