Sequence
atgc intronic sequence ATGC exonic sequence...ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
Basic information
species | Physcomitrella patens |
transcript | PP1S227_69V6.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
----ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
| | | | || | |||||| | | || | || | | | ||||| | ||| | | || | | | ||||||||||||||||| ||||| || ||||| ||||| |||||||||||||| ||||| | | || || | ||| | || |||| |
atgatcagaccttttt-catttcgagatcagaaatgtccaccacatctttatccat---agcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 11
-ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtgga--acagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
||| | | | | | || | | | || ||| | || || | | | | | | ||| |||| | | | | ||| ||| |||||||| |||||||||||||| ||||| || ||||||||| | || | | || || | || || | | || |
tttgtctttttgccccc-tgatattatagttattatacaaaggtacaatttgatc--attgacatcctaaactcgtttaattaaaagagaatattttctgcagAGATATATGGACTCTGAGATAAGGGCAATTATGGCCCAATACATGCCATTGGATAATCAACCAGAGATTTCTAGTCAAGCTCATGAAGGTGTCTAGAAGT
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT2G14720.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------------------------------------------------ttgcatgtctccacaaatggagatctctct--tttgtactagttcgtaaagtgcttgaacttatttgattaacggattt-agcttgtcggtgctgtgga---acagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAA-GCGTAAAGAC
| ||||||| ||| | | | | | | | || || || | | | || | || | | | | |||| |||| |||| |||||||||||| ||||| || || |||||||| |||||||||||||| |||||| | ||| || |||| || || ||| | | |
gtaagctttttattcatccttctgctatttctgttagaagcaaaagattaatgttttatgttttggttgcctgagatgtctcttaaaacattgttttatgtaacccgatatcgtcttggaattgtatcgattacttgggaaaattgttatgaacttgctatgttcatggatttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCACTGGACAGCCAACCTGAGGTCCCGAACCACACGAATGATGAACGTGCCTAAG-
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
-------ttgcatgtctccacaaatggagatctctcttttgtactagtt-cgtaaagtg--cttgaacttatttgatt--------------aacggatttagcttgtcggtgct----gtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAA-GCGTAAAGAC
|| |||| | | | ||| |||| || | || | | | |||| | || || || | |||| | | | ||| || |||| |||||||||||| ||||| || || |||||||| |||||||||||| | |||||| | || | |||| ||| || ||| |||
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG-
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 11
-----ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatt-tagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAA-GCGTAAAGAC
|| ||| | | |||| | || | || | || || || | ||| |||| || ||||| | | | | | | |||| | ||||||||||||||||||||||| || || |||||||| || |||||||| || |||||| || ||||| | ||| | | ||||| | | |
aatgttttaatgagttgagaaattgcaatgtaaggttgacaata-tttgttggtt--ttgcactt-ttggattattgattgatgtttcatggttgcttttt--cagTCATACATGGACTCGGAGATCAGAGCTATAATGGCACAATACATGCCCCTGGACAGCCAAACGGAAGTCCCAAATCATGTCTCTGAGGATCATGCATGAA-
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 11
---ttgcatgtctccacaaatggagatctctcttttg--tactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCAT-CTGACCGAGGAAGCGTAAAGAC
|| || || | |||| | | | | | | ||| | | || | | | | ||| |||| | | ||| |||||| | | || ||||||||| || ||||| |||||||| ||||| ||||||||||| | || | | | || || | ||| | || || | | |||
tgcatggatacctagattaatgtggtacgtgcctgtaattgctatatggaaataggatcaatatgattgtgttaatga---caacttccttttgctgttgcagAG--ATACATGGATTCTGAGATTAGGGCAATCATGGCACAGTACATGCCTTTGGATAATCAAGGAGAGATTCCAAATCATGTTCCCCATGGGGACATTTAGA-
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 11
ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttga-ttaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
| || | ||||| | ||||||| | | |||||| | || | | | | |||| |||||||| |||||||| || || || ||||| ||||||||||| ||||||||| || || || ||||||| || ||||| || | |
------------------------------gtaatatcaattcgtgat-tgcttgatccagcaaaacttaacgttctctactggaaacttttcctg--tagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGATGTGCATCACCACTTGCAAGAGGATGCTTGATTGT
upper sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 11
ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttga-ttaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
| || | ||||| |||||| | | |||||| | || | | | | |||| |||||||| |||||||| || || || ||||| ||||||||||| ||||||||| || || || ||||||| || ||||| || | |
------------------------------gtaatatcaattcgtgct-cgcttgatccagcaaaacttaacgttctctactggaaacttttcctg--tagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGACGTGCATCACCACTTGCAAGAGGATGCTTGATTGTMapped 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|37830974|gb|BJ588986.1|BJ588986EST: CGGAGTTGTNGGCTACGTCGTCTACAAATACAGGCTTCGG TCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
genomic: CGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGGgtatgaactc ... tgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
EST:
gi|208359753|gb|DC946615.1|DC946615EST: TGGCTTCTCTCGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGG TCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
genomic: TGGCTTCTCTCGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGGgtatgaactc ... tgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
EST:
gi|208346052|gb|DC921297.1|DC921297EST: TGGCTTCTCTCGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGG TCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
genomic: TGGCTTCTCTCGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGGgtatgaactc ... tgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTC
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:
33 (upstream exon),
35 (downstream exon)
Score:
15TCAATCATCAAAGCTGGGGTGGGCTGTGTCTTTGATTGTGTTTTTGGGAGTGGCTTCTCTCGGAGTTGTTGGCTACGTCGTCTACAAATACAGGCTTCGGgtatgaactc ... tgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
gattaac putative branch site (score: 15)
aacttatttgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - ctccaca