Sequence
atgc intronic sequence ATGC exonic sequence...ataaacgatttcaatttataattactgtgatgttgatggattgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
Basic information
species | Physcomitrella patens |
transcript | PP1S6_409V6.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
ataaacgatttcaatttataattactgtgatgttgatggattgggt-tgatctcctaat--tcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
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-catgtgggc-caacttctggtttatatta-gcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 1
ataaacgatttcaatttataattactgtgatgttgatggattgggttgatctcctaat---tcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
|| ||| || || | | | ||| | ||| | || ||| | | || | | | || | | | | | |||| |||| |||||||| ||||||||||| || ||| | || |||||||| |||||||||||||| || || |||| | ||||
---aaatattagaacatacgccaatattaagtactatgcaacatgtttccttataaacatgtctagtgaaaggtttactcatgacaattatgtcctccaccagCTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 1
ataaacgatttcaatttat-aattactgtgatgttgatggattgggttgatctcctaattcttg--agctagtgtgattaattggagagagattgtg-cggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
||| | | ||| || || | ||| || || | | | ||| || | |||| ||| | | | || || || | ||||||| ||||||||||||||||||||||| || || |||| || || || |||||||||||||| ||||| || |||||
-taacacttgtaaatggatgaactgatgtaatctt--ctgctcctttcgat-tcaaggtgcttgcctgcttgaataactatttctgctttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
ataaacgatttcaatttat-aattactgtgatgttgatggattgggttgatctcctaattcttga--gctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
| || | | ||| || || | | | || | | | | | ||| |||| ||| | | | | ||| | | | ||||||| ||||||||||||||||||||||| || ||||||| || || || ||||||||||| || ||||| || ||||||
gtgcact-tgtaaatggatgaactgatataatct--accgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 3'ss of exon 1
-ataaacgatttcaatttataattactgtgatgttgatggattgggttgatctcctaattcttgagctagtgt--gattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
||| || || | | || | | ||| | || ||| | || | | || || | ||| ||| | || | ||||||| |||||||||||||| |||||||| || ||||||| || || || || || || ||||| ||||| |||||| ||||
ttctaacaatcgtaaaatttcatgaaagattggttctt---tttggtatctaatttatgtttcgattcggtattcaattgtttgtttccatatgattttgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCTTTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv00s0601g00030.t01 (Vitis vinifera), 3'ss of exon 1
--ataaacgatttcaatttataattactgtgatg--ttgatggattgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtg-cggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
| | | || |||| | | ||| | ||| || || ||| || || | | ||||| | ||| | ||| | | | || ||||||| || |||||||| || |||||||| || ||||||| || ||||| |||||||||||||| ||||| |||||| ||||
tcacatattatgacaatgttttattttctttatgtctttattcattctcttattccctt--ttcttaat---atgtagctcattctattgcttatatgatcgcagCCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
---ataaacgatttcaatttataattactgtgatgttgatgga-ttgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
||| | | |||| | | || | | || | ||| | | | | || | ||| || || | | ||||||| || ||||| ||||| |||||||| || ||||||| || ||||| || || |||||||| ||||| |||||||||||
cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttattt----ttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ07633 (Selaginella moellendorffii), 3'ss of exon 1
ataaacgatttcaatttataattactgtgatgttgatggattgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
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---------------gtaagagcac-gaatcatccatggatttcttcccagctctggtgattgagctc-tctgtctctc---------gctctctcttagTTTGTTCTTCACGCAAGAAATGGAGCTGTCGCTGATTGGACTCCAAAACGCTGGCAAGACGTCGCTGGTGAATGTGATTGCGMapped 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|67577659|gb|BJ949826.1|BJ949826EST: ACTGCGAAGATGATGGGAATATGGGATTCGTTCCTCAATTGGCTCCGCAG CCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGC
genomic: ACTGCGAAGATGATGGGAATATGGGATTCGTTCCTCAATTGGCTCCGCAGgtacgtgacc ... tgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
tgattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaacgatttcaatttataattactgtgatgttgatggattgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG