Sequence
atgc intronic sequence ATGC exonic sequencegtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
Basic information
species | Physcomitrella patens |
transcript | PP1S378_9V6.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagc-atttcaagccttaaactttaa-attgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
| || | | || | | | | | || | | || | | | | ||| | | || | || | | | | ||||||| ||||||||||||| |||||| |||||||||| || | || ||||||||| | ||||| |||||||| ||||| |||||||| ||||| || |
--------------------------------------agtggcggaacattctattactat-tactgattctagtgactgtcctgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
||| ||| | | | | | || | | || | | ||| | ||| | |||| || | || | || | ||||||| |||||||| ||||||| ||| ||| |||||||||| || | || || ||||||||||||||||| ||||| ||||| || ||||| ||||| || |
-----------------------------acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaag-ttatattttgacctgtatatg-catcatgaccttt------cctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 12
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
||||| | | || || ||| || | | | ||||| | | || | | || | |||| || | |||||||| ||||||||||||||||| ||| ||||||| ||||| | || || || || || |||| | | || ||||| |||||||||||||| || |
----------------------------------gtttgttatt-----tttcaggtgcacagtgatgtttc--actgtatttcttttccccactttgctcctctcaggatatccattt---------tgactgcagATTGGGGGAGCTAGTGAAGTTGAAGTTGGTGAGAAAAAAGATAGGGTAACAGACGCTTTACATGCAGCAAGGGCTGCTGTGGAGGAGGGCATTGTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
gtatatcagtcatcctaatttaaatagttgtctcgtttgaca-atgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgc----ttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
|| | |||| | || || || || || | || | || | | | || || | || | || | | | | || | ||||||| | || | | || | ||||||||||||| || |||| || ||| |||||||||| || | || || |||||| ||||||| || ||||| |||||||| ||||||||||| || |
gtgaggttattgacctactgtatgtattta---cgaatggtagattacatgttcttgttttatatcgtaattgtaataactgtt--acctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
| | || |||| || ||| || ||| ||| | | | ||| | ||| || || | | | | || || | |||| || || |||||||||||||| ||||||| ||| ||| |||||||||| || | || ||||||||||| ||||| || || || ||||| ||||||||||| || ||||
-----------------gtatgcctacttgtgtcattt-----tgg---ttaatggtttatccc--tggtg-----aacatccca---ctgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
| |||| ||| || | || || | | | | |||| | || || ||| | || | | || || |||||||||||||| ||||| | ||| ||| |||||||||| || | || || ||||| || ||||| ||||| || ||||| ||||||||||| || || |
------------------------------gtttgtttatt--tgagtttaccttgcttgctgttaagtcttatctggtgcttcatcatatggttttgtcatgataaa-attaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
||| | ||||| | | || | || | || || | ||| ||| |||| | | || || ||| | || | | | || |||||||||||||| ||||| | ||| ||| |||||||||| || | || || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||
--------------------------gtttgtttatttga--gtttaccttgcttgc-tattaggattttatctg--gcacttcatcctatggttttgtcatgataaa-actaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttca-agccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
| | || | | ||| | ||| | | | | ||||| | || | ||| || | ||| || | | |||| |||||||||||||| ||||||| ||| ||| |||||||||| || | || || ||||| || ||||| || || || ||||| ||||| |||||||| | |
----------------------gggggccgctacggccgctattgacaactat-gatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaac-------tgcccttct--------gcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
||| | | | | |||| || | || || ||| | | | || ||| | | ||| || | || | ||| ||| ||| |||||||||||| ||||||| ||| ||| |||||||||||||| | || || ||||| ||||||||||| ||||| || ||||| ||||| ||| | || |
--------------------------gttagtccatgttataatg----ttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctg---gagctaatt---------gtgttta--gATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
upper sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
--gtatatcagtcatcctaatttaaatagt--tgtctcg-tttgacaatg----aaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
| ||||| | | | || | | ||||| | ||| | | ||| | | || ||| | | || | | | | | || | || | || | || || || ||||| |||||||||||||||| ||| ||||||||||||||||| | ||||| ||||| | ||||| || || || ||||| || || || ||||| || |
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagc-tactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAGMapped 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|162171070|gb|FC346969.1|FC346969EST: AATTGCAGGAGAGGTTGGCCAAATTGTCAGGAGGTGTAGCTGTACTTAAG ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACT
genomic: AATTGCAGGAGAGGTTGGCCAAATTGTCAGGAGGTGTAGCTGTACTTAAGgtatatcagt ... gtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACT
EST:
gi|162211030|gb|FC387336.1|FC387336EST: AATTGCAGGAGAGGTTGGCCAAATTGTCAGGAGGTGTAGCTGTACTTAAG ATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACT
genomic: AATTGCAGGAGAGGTTGGCCAAATTGTCAGGAGGTGTAGCTGTACTTAAGgtatatcagt ... gtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACT
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:
24 (upstream exon),
35 (downstream exon)
Score:
5ATCCGAGAGGCCATCAGCACTGCCACTTCCGATTACGACAAGGAGAAATTGCAGGAGAGGTTGGCCAAATTGTCAGGAGGTGTAGCTGTACTTAAGgtatatcagt ... gtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
ttttatttctttcttt CT-rich tract
ttaaactttaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG