Sequence
atgc intronic sequence ATGC exonic sequence...ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
Basic information
species | Physcomitrella patens |
transcript | PP1S147_10V6.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
--ggagtattggattctctg-gtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
|| | || || || | | | | | |||| | | || || | | | ||||| | | || |||| ||||||| | ||||||| || |||||||||||||||||||||||||| ||||||||| |||| ||||||| || || |||||||| ||||| | || || || || || |
agagaaaaaaaaatgctgtgagcattacttaaatctgcagtt-tgttaccttatagtctttccaatgcttattatgtca-attttcattgtgaatttg-gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
-ggagtattggattctctg-gtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
|||| | || || || | | | || | |||| | ||| || | | | ||||| | | || |||| ||||||| | ||||||| || |||||||||||||||||||||||||| ||||||||| |||| ||||||| || || || ||||| ||||| | || || || || || |
aggagaaaaaaatgctgtgagcattacttgaatctgcagtttgtttaccttatagtctttccaatgcttattatgtca-attttcattgtgaatttg-gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
ggagtattggattctctggtccaagtagagtatgcattgatttt-gttttctggaaggctagaaaacaattat-ataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
| || ||| | | || | | || ||| | | || ||| | | || |||| ||| | | | ||||| ||||||| || |||||||| ||||||||||||||||| || |||||| |||| |||||||||| || || ||||| ||||| | || || || || || |
-gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttc-atagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
-ggagtattggat--tctctggtccaagtagagtatgcattgattttg-ttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
|| || ||| | | | || | | | | || || | || | || | ||| | ||| | ||| | | | |||||| ||||||| || |||||||| ||||||||||||||||| ||||||||| |||| ||||||| || || || ||||| ||||| | || || || || || |
gggtgttttgcttggtatttgaacttaatgctg-atctgctggtagtgatcttattgaatttctaatgcttattgcgt--catttttttaattaattttaa-agGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
------------ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
|| ||||| | | ||| |||| | | ||| ||| | || | | | || | || | | | || || |||| |||||| |||||||||||||| ||||| | ||| ||||| ||||| ||||| |||| ||||| || || ||||| ||||| ||||| ||||||| || |
attgggaaatgtagaacattggcaacaagtg-ccagatagactgttgattagtttgttattttctgttgtttga---ctgctaattctctttattattatgaa--------gGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
----ggagtattggattctctggtccaagtagagtatgcattgatt-ttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
||| | || | | ||||| | || | | | || ||| | || |||| ||| || | || || ||||||| |||||||||||||| ||||| | ||||||||| ||||| ||||| |||| || || || || ||||| ||||| ||||| ||||||| || |
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattac-taat----tctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
-------------------------------------------------------ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaac--aattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
| || | | | || | || | | | | || || || | |||| || | | || |||||||| | |||| || |||||||| ||||||||||| ||||||||||||||||| |||| ||||||| || ||||| ||||| ||||| || || |||||||| || |
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgat-ttgaatttt-gtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
ggagta-ttggattctctggtccaagtagagtatgca--ttgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
| | | | | || | || |||||| | |||| | | || | | || | | | | | || || | || | ||||||| ||||||||||| |||||||| ||||||||||| || || ||||| |||||||||| || || ||||| ||||| | || ||||| || || |
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttg-atcttggatattttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
upper sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
| | | | | |||| | | || | || | | ||| || | | | | |||||||| |||||||| || || ||||| || ||||||||||| || || || ||||| || || || || ||||||||||| ||||| | || ||||| |
---------------------------------gtaaggctatagtttctggttatactcta---tctttggttggtctaatc-tgtt-attaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCACMapped 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|162194819|gb|FC370509.1|FC370509EST: CCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAG GTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTT
genomic: CCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggatag ... atttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTT
EST:
gi|162199498|gb|FC373787.1|FC373787EST: CCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAG GTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTT
genomic: CCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggatag ... atttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTT
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),
29 (downstream exon)
Score:
8GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatggatag ... atttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
atataac putative branch site (score: 8)
tttttgc putative PPT
tagaaaacaattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG