Sequence
atgc intronic sequence ATGC exonic sequencegtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S52_245V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaac-tgtaat--gtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| | | || || |||| |||| | |||| || ||| | | | | ||| || ||| | || || | ||| | | || | ||||| || |||||| | || |||||| ||||| |||||||||| || |||||||| ||||||||||| || ||||||||||||| ||||| ||||||
----------------------------------------------------------------------------gttatgtgagattgcttt--tttagttt------tttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataactatgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgt-cgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
|| |||| | | || | | |||||| | | | ||| | | | | || ||| ||| | ||| || | || | | |||| || | ||| | || |||||| || || | || ||||| || ||||||||||| ||||||||||| ||||||||||| ||||| || | ||||
----------------------------------------------------------------------------actcactgattccaatactgtttggttt----gttttactttgttgtaatactgttgcctt--agttgtttgttttgtacttgaacttatcgcctgccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| ||| | || || ||| | | | |||| | | | || | | | || |||| | | ||| |||| | | | || ||||||| | |||| | || |||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||||||||||| | ||||||
----------------------------------------------------------------------------aacaaaagaatgaacgatg--ttaatgctggactttttgtgtattgccattgtgcaatgggtg--ttgtctgtgtt-tgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
|| |||| ||| | | || | | ||| | ||| | | || | || |||| || ||| |||| | | | || |||| || | |||| | || |||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||||||||||| | ||||||
-------------------------------------------------------------------------aacagtcaaagatgttaatgc----tggactgttgagtttgtgta---ttgccattgtgcaataggtgttgtctgtgttggt-tgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaact---gtctaattcttggtattctagcttt----agatccgag-attttactttgacttagagtcgtagttttaggg--ggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
|||||| ||| | | || | | | | || | | | ||| || | | | | ||| || ||| || | || || ||| | | ||| | | | | ||||| | || | || || ||| || || |||| || | ||| | || |||||| ||||||| | ||||||||||| || ||||| || || ||||| || ||||||||||||||||||| | ||||
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcattttagttggtg--ttgatcacgat--tgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| || |||| ||| | | || || | | ||| | | || | ||| | | | | | || | | | || || |||| || | | || | ||| | | | | || | || ||| |||| || | |||| | || |||||| || || ||||||||||||| || ||||||||||||||||| ||||| ||||| ||||| |||| ||||||
------------gtactctttttcttct--------acacattttga----tttgatt-tggacat----gatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaattt---ggtctaagactttctgctttatgtgattctaatttt---gaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggt-attctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| | || |||||| || | | | ||| | || | ||||| | | || |||| ||| || | | ||| | | | | | | | | || | || | || | ||| | |||| || | ||| |||||||| ||| | || | || || ||||| ||||||||||| |||||||| || |||||||| |||||||| || ||||||
------------gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaat---agataacgtgacgacctattgaca-agtatcaacaatcgtctgttttgttaccctcacact--ctctgatactac-atgtctaaaaccatttttga-agGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| | | | | | || ||| || | | | | | || || || | | | ||||| | |||| | |||| || | | | ||||| || | || | | |||||| |||||| | || |||||||| || |||||||| |||||||| ||||||||||| |||||||| | | ||||
-------------------------------------------------------------------ttgattcttggtgc---atcttatttcaattctctattgagggtt-----gggttaattgatgtggtttat-acttaaaaaaggttaatcagcgttttgttgtttc-----cagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 1
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgat--aacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttcca----acagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| ||| || | | ||| | ||| ||| || | || | | | ||| | ||||| || | ||| | ||||| ||| ||||| ||||| || || |||||||||||||| |||||||| || ||||| || |||||||||| ||| ||||
---------------------------------------------------------------------------------------------------------------------gtattctatccatcgcctttttccaatgaacaacaaactaagatcgctctttttctttttccctttgcagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGA
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 1
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgat--aacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
| ||| || | | ||| | ||| ||| || || | | | | | |||| || | ||| | ||||| ||| ||||| ||||| || || |||||||||||||| |||||||| || ||||| || |||||||||| ||| ||||
---------------------------------------------------------------------------------------------------------------------gtattctatccatcgcctttttccaatgaacaacaa-------acttcttttttttccttttgtagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGAMapped 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|18348574|gb|BJ180623.1|BJ180623EST: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAG GGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
genomic: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAGgtaacctgct ... tttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
EST:
gi|18354034|gb|BJ186089.1|BJ186089EST: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAG GGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
genomic: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAGgtaacctgct ... tttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
EST:
gi|162277342|gb|FC453148.1|FC453148EST: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAG GGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
genomic: AAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAGgtaacctgct ... tttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAG
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:
32 (upstream exon),
27 (downstream exon)
Score:
8CTCTGGGAAGGATATCAGGTTCGGAGTTGAGGCTCGAGCTCTTATGTTGCAAGGTGTGGAGCAACTTGCAGATGCTGTGCAAGTGACCATGGGCCCCAAGgtaacctgct ... tttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
aattaac putative branch site (score: 8)
ttgtgctctctttcc putative PPT
aattaact TA-rich tract