Sequence
atgc intronic sequence ATGC exonic sequencegtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
Basic information
species | Physcomitrella patens |
transcript | PP1S44_102V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
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------------------------------------------------agtttcttgtagaacact----aaaaggagtccttgcttagttatgctttatgcctgatgtt---ttctttatcaacaaaacaatcatatttttttctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttct--gttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
|| || || ||| || || || ||| | | | | | | || |||| | | |||| |||| | ||||||| || || ||||| ||||| |||||||||||||| |||||||||||||||||||| || ||||| ||| | |||||||| || | || ||||| |||||
---------------------------------------------------------tatatttgcccttaaaatgattaatgaattgtttgaccgtgtgctgcttgagagttttaacactgattttgataatatatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
||| | || | || | | || || || || | | | || | | | || |||| | ||||| |||| ||||||| || || ||||| ||||| || ||||||||||| |||||||||||||||||||| || ||||| ||| | |||||||| || | || ||||| |||||
------------------------------------------------------atc-atattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttc---tgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
|| | ||| | | | ||| | | || | || || || || || || | ||| | | | || || | || |||| || ||| |||| || ||||||||||||||||| || ||||| ||||||||||| || || || ||||| ||||||||||| | |||||||| || ||
-------------------------------------------------------cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaag---gtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
| | ||||| | | | | | | | | ||| |||| || | || || | |||| | || || || || || | |||| || || | || || ||||| ||||| ||||| || ||||||||||||||||| || || || ||||| ||||| ||||| | || || || |||||
---------------------------------tttccattggta----gcttttttttggtgaagc----aacatttttccaagttttgt---atatttattcaaaattattttctaaaccaatgtgatcatggaatgtt-----------cagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaa--gattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
| |||||| | | |||| | |||| | | ||| ||||||||||| | || ||||| ||| | || ||||| |||||||||||||||||||||||||| ||||| | ||||| || ||| | || ||||| || ||
------------------------------------------------------------------------------------------------------------gtatgtccttccaattcaggctcagcgctgattttatcgatggtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG
upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
gtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctc--tgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
| |||||| | | |||| | |||| | | ||| ||||||||||| | || ||||| ||| | || ||||| |||||||||||||||||||||||||| ||||| | ||||| || ||| | || ||||| || ||
------------------------------------------------------------------------------------------------------------gtatgtccttccaattcaggctcaacgctgattttatcgatggtttcagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGGMapped 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|22133115|gb|BQ827551.1|BQ827551EST: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAG GCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
genomic: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcct ... tctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
EST:
gi|22492681|gb|BU052604.1|BU052604EST: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAG GCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
genomic: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcct ... tctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
EST:
gi|22492244|gb|BU052167.1|BU052167EST: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAG GCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
genomic: CAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcct ... tctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGA
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:
35 (upstream exon),
33 (downstream exon)
Score:
43TTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcct ... tctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcagGCATTACTTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGG
ttctgttttctgtt CT-rich tract
tacattt TA-rich tract