Sequence
atgc intronic sequence ATGC exonic sequence...tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
Basic information
species | Physcomitrella patens |
transcript | PP1S2_667V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgattt-cacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
| | | | || || || | || ||| |||| | | | || || || | | ||| | || ||| | ||||| || ||||||||||| ||||||||||| | |||||||| || || |||||||| ||||||||||| | ||| | |
-----------------------gtttgccaccttgaatctcacttgttctgcttttactgtgtcaattggtaccttac-agtcttggtgtttgtat-cagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctg----ttgattttgtgtagGCACTTGGA-AAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | | | || | | ||| | || | | ||| | ||| | || | | || |||||| || ||| | || | | | ||||| ||| ||||| || ||||||||||| |||| |||||| | |||||||| || ||||||||||| ||||||||||| | ||| | |
--gtttgtaaacttggaactctaca----tctggttcctgtgttctg---tttatatatgacaat----ttacatgatgatctccaccttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctg----ttgattttgtgtagGCACTTGGA-AAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | | || | | || | | | || ||| | ||||| || || | | || |||||| || ||| | || | | | ||||| ||| ||||| || ||||||||||| ||||||||||| | ||||| || || ||||||||||| || |||||||| | ||| | |
--gtttgcaatcttgagctctg---cacctggatcctttgtgatctg-cttgtat--ttgacaat----ttacatgatgatctccaccatttggtgttctatcagGGCTTGGGCAAGCACAACATCATTTGCATTGAGGATCTTGTTCATGAGATCATGACTGTCGGCCCACACTTCAAGGAGGCGAACAACTTCCTTTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6
--tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
||| | | | | | | | || | | | | || | | | ||| ||| ||||| | | | || || | | || ||| || ||||| || |||| ||||| || ||||||||| | ||||||||||||||||||||||| |||||||| ||| | ||| |||
gtccgtgtggtctattctgtagtc-ctctgtaaacacttccattgcttgtttgttctattacttagtttttttccctgacataacat-tcaatgcc----agACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttg--tgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
| || | ||| | || | | | ||| | | | ||| | ||| | | | || | |||| || || |||| || ||||||| | ||| ||||| || ||||||||| ||||||||||||||||||| ||||| || |||||||| | ||| | |
----------------------gtattgtttattttacaat--tcttccttacagatttt--aattaattcgctacatgcttcttacttgcttggatgacagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | | | || | || | || || | || | | || | | | | || | ||| || || | | || | | || ||| || ||||| || |||| ||||| || |||||||| || |||||||||||||| |||||||| |||||||| ||| | ||| |||
--gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctat-tactcagttttttcgctgacataacattcaatgc---cagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------------------------------------tcgtataaatagctgcattgcgacacaattaa---aattagtaggacctgacgtgtatcctttgca----gtgatttcacctgatgaat---tctgttgattttgtgt-agGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|||| | | | ||| || ||||| || || | || | | |||| | | || ||| | || | || ||| | ||| | ||| || |||||| || ||||| || |||||||||| || ||||||||| | || ||||| || || |||||||||||||| |||||||| ||| | |
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttg-gattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtag-gacctgacgtgtatcctttg--cagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT-------------------------------------------------------------------------------
| | | | || | | | ||||| | |||| | | | | || ||| || | | | |||| ||||||||| |||||||| || | ||||||| | || || ||||| | || || |||||||| |||||||||||||||||||| | ||| | |
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatc----aggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtag-gacctgacgtgtatcctttg--cagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
| | | | || | | | ||||| | |||| | | | | || ||| || | | | |||| ||||||||| |||||||| || | ||||||| | || || ||||| | || || |||||||| |||||||||||||||||||| | ||| | |
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatc----agGCTCTTGGAAAGCATGGTATCATTTGCACTGAGGATTTGATCCACGAGATTCTAACAGTAGGACCTCATTTCAAGGAAGCCAACAACTTCCTTTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00150.t01 (Vitis vinifera), 3'ss of exon 1
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
||||| | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| ||||||||||| ||||| | |
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgt-atcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | ||| | | | | | | || ||||| | || || | | | || | || ||||| | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| ||||||||||| ||||| | |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00070.t01 (Vitis vinifera), 3'ss of exon 2
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtg-tagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| || | ||| | | | || ||||| | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| ||||||||||| ||||| | |
--nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 5
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgt-atcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | ||| | | | | | | || ||||| | || || | | | || | || ||||| | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| ||||||||||| ||||| | |
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctatatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 6
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatga-attctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
| ||| || ||| ||| || | | || || | | || | | || || | |||| ||| || | || || |||| | || ||||| || ||||| || ||||| |||||||| |||||||| | |||||||| || ||||||||||| || |||||||| | ||| | |
------------gtttgttgtaggttaaataacatttatatgttc-gatgtat-tgctataaactggcttttc--aatgacattttggtatgttattgcagGCTTTGGGCAAGTTTGGAATCATTTGCATTGAAGATCTCATCCATGAGATTATGACTGTTGGGCCACACTTCAAGGAGGCAAACAACTTCCTGTGGCCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
|| | | | || || ||| | || ||||| | || || | | | || | || ||||| | || ||||| || || || || || || ||||| |||||||| ||| | |||||||||||||| || ||||| ||||||||||| |||| | |
----------------gtttttatgtcctgtatcttggttttttttgaggg--attgtttgctatatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 5
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttca---cctgatgaattctg--ttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
||| | | | | ||| ||| || || |||| ||| | || || || || |||| || ||||| ||||| ||||||||||| || ||||||| ||| ||||| || ||||||||||| || || ||||| || ||| |||
---------------------------------------------gtacgatccttttctacgatgacttctagttctcatcgtttcttatttgttctttctcagAGCCTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTTGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTTMapped 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|162169492|gb|FC346056.1|FC346056EST: GGTTGTCAAGTCCACGTTTCGCCCTTACTGCCATTACCATTTTCGAGCAG GCCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGAT
genomic: GGTTGTCAAGT-CACGTGTCGCCCTTACTGACAATACCATTATCGAGCAGgtaccgtcct ... ttttgtgtagG-CACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGAT
EST:
gi|162220042|gb|FC396519.1|FC396519EST: AGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAGCAG GCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATC
genomic: AGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAGCAGgtaccgtcct ... ttttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
ttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - agctgca