Sequence
atgc intronic sequence ATGC exonic sequencegtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
Basic information
species | Physcomitrella patens |
transcript | PP1S55_132V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
| || | | | | || | | | | | | |||||||| |||| | | || || ||||| ||||| || ||| || || ||||||| | || ||||| || || || ||||||||||| ||||| ||||||||||||||||||||| ||| || || || || || | | || |
-------gatactcttctattttcttgatgtatt--ctgtcgttcagcatgatgattaaactagagaatgatcaatg--tcattgattatactttt-actgctcactc----acagGTGCGTGAGATGCCGAATGTATTAATTCTTCCTCGAAGTGCAGATTACAGTGAAGAAGTGTGGATTGAAATCAGAGAAAAGGCACTCGCAATATTGCAAT
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
| ||| ||||| | ||| || | | ||| ||| || ||| |||| || |||| || | | | | ||| | | | |||| ||||| ||||| || || || ||||||||||| ||||| || |||||||||||||||||| || ||| || ||||| || | | || |
-----------ttttctgcattgcta-tggtggtgccacttgttcatcatccatctta--taaaaaaagaacttgttgttcagcaa--aatgatggatactatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------gtacag-cgctatcttcatgtctgctaacagct-tcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaatta---tttgttc-----------gact--tctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
|||| | | || || | | | || || | ||| | | | || || | | || | | | ||| ||| ||||| ||||||| |||| || |||| || ||||||| |||| ||||| || || || |||||||| || ||||| || |||||||||||||||||| || ||| || ||||| | || || | |
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
|| || | | ||| |||| | | | | | | | | || || |||| | | |||| | | |||| ||||| || || ||||||| | || ||||| || || || ||||||||||| ||||| || |||||||||||||||||| ||||| || ||||| || | | || |
--actttgcacttgtgatgcttgctg-tacttataatacgctaatagaa--aagtcatgtttcaaacaaat--gatttaatacttgttatgtgttca-----ttgatc----acagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
|| |||| | | || || || || | | | | | ||| | | | ||| ||| | || | | | | | | | ||||| ||||||| ||| ||||| ||||||||||| |||||||| ||||| |||||||||||||| || ||| || ||| | ||||| | ||| | ||
-------ctcataatcatatata-tattagatt-acgtctgtcagtctacaac----aatgatagttttaatagatagattat-actaacatactttg--tgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattaca--aatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
||| | | | ||| || |||| |||||| || | |||| | | | | || || | | || || || || || | | || || | ||||||| ||||||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| ||| |||||| | || || ||||| | || |
gtatgactttcttttccagtg-actaa--acttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattg-cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
| | || | ||| | || | | | || | ||| | || | ||| ||||||| | ||||| | ||||| | ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| ||| |||||| | ||| | | | | | |
-----ggaaaaataaaatagccatacacaatatttt--ttatgagttaacaattctgcattgtatatcaaggcgat-----gttaattagccccatcatgactttgctt----cagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
upper sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgactt--ctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
|| | ||| || || || || | | |||| || || |||||| ||||| ||| | |||||||| ||||||||||| ||||||||||||||||| || | |||| || || || | || || | ||| ||||| | |
-------------------------------------------------------------gtaagcacc-tggtttttttatgcgacatgtttggaacttgactcgtgtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGTMapped 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|37840918|gb|BJ598926.1|BJ598926EST: CTGGCTGTGCCCTGGACGGTATCGAAGGCCCCCAGTGGCTAGAAGCTTGG GTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
genomic: CTGGCTGTGCCCTGGACGGTATCGAAGGCCCCCAGTGGCTAGAAGCTTGGgtacagcgct ... tcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
EST:
gi|67508082|gb|BJ940953.1|BJ940953EST: CTGGCTGTGCCCTGGACGGTATCGAAGGCCCCCAGTGGCTAGAAGCTTGG GTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
genomic: CTGGCTGTGCCCTGGACGGTATCGAAGGCCCCCAGTGGCTAGAAGCTTGGgtacagcgct ... tcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
EST:
gi|67579412|gb|BJ951533.1|BJ951533EST: CTAGAAGCTTGG GTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
genomic: CTAGAAGCTTGGgtacagcgct ... tcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGT
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:
30 (upstream exon),
34 (downstream exon)
Score:
3CCTGCTGGATGACTGTGCGATGAAAGAAGCGCTCATCAATGGCACTATTGCTGGCTGTGCCCTGGACGGTATCGAAGGCCCCCAGTGGCTAGAAGCTTGGgtacagcgct ... tcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
cattaat putative branch site (score: 3)
cttctttgtctt putative PPT
attcttcattaattat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG