Sequence
atgc intronic sequence ATGC exonic sequenceTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa...
Basic information
species | Physcomitrella patens |
transcript | PP1S46_53V6.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgta---ctattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaag-gtaaatgcacgtaa
| || | |||||||||||||| ||||| || |||||||| ||||||||| | || |||||||| || | ||||| || |||||||| ||| | ||||||||| | ||| |||| |||| | || | |||| ||| | | | ||| | | |||||| | || | || | |
TGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCCTGATGCAGgtaactccattgtgcttcttttcttttaaacatgcaaaacagtcctttgcattat-taactgatagtgtctgagagcaggggatcagcctgcaagtccttt---
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa
| | | |||||||| ||||| || |||||||| ||||| ||||||||||| || ||||||||||| | || ||||| || || |||||| | ||||||||| | | | | | | | | | || |||| || || | || | | | || | || ||| | | | |
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgta--actgatggatgtgtgtgtgtttt-ttaaaagaaaatatacaaaccttctc--taacattg-cttctttttctctcctgatag-------------
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 6
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtac-tattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactga-----gatttttatagcaaaggtaaatgcacgtaa
| | ||||| ||||| |||||||| ||||| |||||||||||||| || || || || || ||| ||||| | ||||| || ||||| |||||||| |||| ||| || | | | | | ||| | | | | | | | | | | | | | || | | |||
AGTTCTCTACTCTTCAGTCGTCTATCCTCACAACTATGGGTTCATTCCTCGCACGCTGTGCGACGATAGTGATCCTTTGGATGTGCTGGTCATAATGCAGgtgtgtatttc---cttgcacgttgctaaatcagaatacaataagtctttcatctaggtatagcccatccatacatggtcccttcactgaaacttgttacaca---
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactg--agatttttatagca-aaggtaaatgcacgtaa
|| | |||||||||||||| || || ||||||||||| ||||||||| | ||||||||||| || | || || || ||||| | ||| | |||||||| || ||| | ||| |||| | | | | ||| | |||||||| | |||| | | ||| || | |||| || |
AGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCCTGATGCAGgt--tagtca-gtcttccttttcccacttgtctgtgtcatgtggggacatttgtgaagaatgtagagtattcactctttgtattacaaggcccttgtttctgt
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G061928_T02 (Zea mays), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactga--gatttttatagca-aaggtaaatgcacgtaa-----
|| |||||||||||||||| || || ||||||||||| ||| ||||| | ||||||||||| || | || || || ||||| | ||| | |||||||| || ||| ||||| | | | | ||| | | |||||||| | |||| | | ||| | | ||||| | |
AGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCCTGATGCAGgtt-------agtcttcctttttccacttgtctgtgtca-tgtggggcatttgtgaagaatgtagagtattcactctttggattacaaggtccttatttctgttcagg
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa--
||| | |||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||| | |||||||| ||||| | || |||||||||||||| | || | | || | || | ||| | | ||| || | | | | || | | ||| | | | | ||
TATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATTCCACGTACTATTTGTGAGGACGGTGATCCCATGGATGTCTTGGTTATTATGCAGgtact--tgaatattgttcatattgccaacttcttgctagttagtgtgattcaagttttctgaaaatggattgtgtaataagtcaacaacttccgttcaact
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA03G33000.4 (Glycine max), 5'ss of exon 7
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa---------
| | | |||||||||||||| ||||| |||||||||||||| || ||||||||| |||||||||| |||||| | ||||| | | |||||||||||| | | | | || || |||||| | | || | | ||| ||| | | ||| ||| | || |
TGTTCTTTACTCATCAGTTGTGTATCCTCACAATTATGGGTTTATCCCACGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtattt------atatatccgttgatatatcaaattttccc---cggatgtcttcaataagacatgcatgcattcttacgattgtctgcatctcattttttttgtctac
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA10G05130.1 (Glycine max), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa----
|||| | |||||||| ||||| ||||| ||||| |||||||| || ||||||||| |||||||||| | |||||||| ||||| | || || ||||||||||| | || | || | || ||| | | ||| ||||| ||| || | | | || | |||| | | |
TATCCTTTACTCATCGGTTGTGTATCCTCACAACTATGGGTTTATCCCACGTACTATTTGTGAGGACGGTGATCCCATGGATGTCTTGGTTATCATGCAGgtact--tgaatcttgttcatattgtcaacttcttgctagttagtgtgccttgtg--tgatattaagttttctgaaaatggattgtgtaattagtcaacaactt
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 7
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgt----attttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa
| | |||||||||||||| ||||| ||||| |||||||| || || |||||| |||||||||| |||||| | ||||| | | |||||||||||| | | | | || | || | | | || | || || || ||| || | | ||||||| | | | | ||| |
CGTGCTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATCCCTCGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatatatccgttcatattatcaaattttccttgtaaatcagtgggcatcgtgtatatatttaaaaatgagattactttcaaactgacaaactttc----
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgt-attttgtgaatga-gatagactgagatttttatagcaaaggtaaatgcacgtaa-
||| | |||||||| || || || |||||||| |||||||||||||| ||||| ||||||||||| || || ||||||||||| ||||||||||||||| || | ||| | || || | || ||| | | | || | | | | | ||||| | | | | | | | |
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacat---attttttcatacaattttgagaacctgcataattcattacataatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 5'ss of exon 4
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgta-cta---ttcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa
||||||||||| || ||||| |||||||||||||| || ||||| ||||| || | ||||| || | ||||| ||||||| || ||| ||||||||||| || || | | | | | | |||| || |||| || || | |||| ||| | |||| | |||
GATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCCTTATGCAGgtaactgtgttttcacaaccatcaaaattatcatcaaatacca-catt-gtgttgta-acctgagttagcttctgattcgtgtag-------------------
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 5
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa-
| | ||||||| |||||||| || || ||||| ||||| || || ||||||||||| |||||||| | || ||||| ||||| | || || ||||||||| || | | ||| | | ||| || | | |||||| | || | || | | | || | | ||
TGTGCTGTACTCTTCAGTTGTGTACCCCCACAACTATGGCTTTATCCCACGTACTCTCTGTGAGGACAATGACCCCATGGATGTCTTGGTTATCATGCAGgtatgcttaatgctgtttgacatgtgtcactgttttgaatgcgtcatattttcacctgtatgctgattacaatgcatgtt-tggaaacaattttatttatcMapped 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|208349328|gb|DC910387.1|DC910387EST: GTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAN GAACCTGTTTTGCCNGNTGCGTTCGTTCGAGCAAGAGCTATTGGGCTTATG
genomic: GTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattca ... ttgcttgcagGAACCTGTTTTGCCTGGTACGTTCGTTCGAGCAAGAGCTATTGGGCTTATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgtattttgtgaatgagatagactgagatttttatagcaaaggtaaatgcacgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT