Sequence
atgc intronic sequence ATGC exonic sequence...caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
Basic information
species | Physcomitrella patens |
transcript | PP1S47_161V6.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
caggggctgttcttgaaatatgttgaaaggattatccat--ctttgg-gtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgt-gtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| | | ||| | ||| | | | | ||||| | | | | |||| | || | || | |||| | | ||| || ||||| |||||||| ||||| ||||||| ||||||||||||||||||||||||||||| || ||||||||||| || || || || ||
----ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaata-agtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| || || | || | || | || | | | || | | | | | | | | | | | ||| | || | |||| || ||||| ||||||||| ||||| | |||| || || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| |||||
tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttg-cagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
---caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatga--catagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| | || ||| || ||| | | | ||||| | | || | | || | ||| | | || | | |||| || ||||| |||||||| || || ||||||| ||||| ||||||||||||||||||||||| || || ||||| |||||||| || || ||
gtcttgaaagagatcctgatttaacttgccatcagaaat-gcctttgaaattttcccaagtctaacgtttgttcactgccaaatatt----aatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM5G812228_T01 (Zea mays), 3'ss of exon 10
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| | || | || | | || || || || || | | | | | || | | |||| |||||| |||| |||||||| |||||||| |||||| | || || | |||||| | |||||||| || ||||||||||| || || |||||||||||||| |||||
-gttagttatttccgcaacttcaacacagatgggggtattcatgagtttatcttggaataatcgttctaattaaaatagtctt-gtgatg-------cagGAGATATTGGCGAGTGGCAGCCAGATGGATCCTTAAAAGTGATTGATAGAAAGAAGAATATTTTCAAGCTTTCGCAGGGGGAATACGTTGCAGTGGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
caggggctgttcttgaaatatgttgaaa----ggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| | || || | || || | | | || || | | |||| | | | | | | |||| | | | |||| |||||||||||||||||| | || |||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||
-----gttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttat-taacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
------caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
|||| | ||| |||| ||| | | | | | | || | | | || | | |||| | | | |||| |||||||||||||||||| |||| |||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||
gttatttcatttatgttttccaaa---attgaggtttatattcttatattagctgttgggttgggtcacaattttccttttat-tcacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtat-cagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
| | || | |||||| || | || | | || ||| | ||||| |||| | | | || | | | || |||| |||||||||||||||| | |||| | |||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| || |||||
---gttcatttttcagtttatgtttgaataag-atatgcttctacgtggat-------tgcatgat--catattttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
caggggctgtt-cttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtca-atgatgacatagacaagttctttgtgatgtgtgt-atcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
|| || ||| ||| || || |||| || || | | | | || | || || || || | | || | | | | ||| ||||||||||| |||||| ||||||| | ||||||| || ||| | |||||||||||||||||| | |||||||| ||||| ||||| || |||||
-agactctaaaacttagtctatattttaaccattag--attgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA
upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatg-atgacatagacaagttctttg-tgatgtgtgtat---cagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
||| | ||| || | || | |||| | || |||| | | || || | | | |||| | || ||| | | | | |||| ||| |||| ||||||||| ||||| |||| ||||| || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||
-gtttgctcatattggcatttcttctt-gaattaa--gttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAAMapped 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|6102274|gb|AW126744.1|AW126744EST: ACGACCGGAGCTCACGGAGGAGGTTCTTATCAATGGTTGGTTTCACACAG GCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCA
genomic: ACGACCGGAGCTCACGGAGGAGGTTCTTATCAATGGTTGGTTTCACACAGgtacgccttg ... tgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCA
EST:
gi|162167248|gb|FC342813.1|FC342813EST: ACGACCGGAGCTCACGGAGGAGGTTCTTATCAATGGTTGGTTTCACACAG GCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCA
genomic: ACGACCGGAGCTCACGGAGGAGGTTCTTATCAATGGTTGGTTTCACACAGgtacgccttg ... tgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
tgaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA