Sequence
atgc intronic sequence ATGC exonic sequence...tttagattgcctgcaggcaacctaatgcgcttgaattagtgttgggcgttttcttttgctttaccggacgttgccaacggtagcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
Basic information
species | Physcomitrella patens |
transcript | PP1S68_31V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 8
tttagattgcctgcaggcaacctaatgcgcttgaattagtgttgggcgttttcttttgctttaccggacgttgccaacggtagcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
|||| | | | | | | ||| | || | | || |||||| | | || | || | || | ||| | ||||||| || | |||| |||||||||||||| ||||| ||||| |||| |||||||||||||| || ||||| ||||| ||| | || |
gttagtctactcaattttagcatcaaaaccttagccctttattac-caaaatgttgtgctttgt--gtccttat-attggc--ccttttactgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G104254_T02 (Zea mays), 3'ss of exon 4
tttagattgcctgcaggcaacctaatgcgcttgaattagtgttgggcgttttcttttgctttaccggacgt-tgccaacggtagcacctt-gtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
|| | | || | || | | | ||||| || | | | | |||| | || | ||| | ||||||| || | |||| ||||| |||||||| ||||| ||||| |||| |||||||||||||| || ||||| ||||| ||| | || |
--------------------gttagtcatttcattttggcattcaaaccatagctctttattaccaaacatgttcttatattagctcttttactgttattagATACCAAGGAAATTCACAAGCATGACAGAAGGGAAGATGGGCTATGAAGACTTTGTTTATTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------tttagattgcctgca----ggcaacctaatgcgc-ttgaattagtgttgggcgttttcttttgctttaccg--gacgttgccaacggta-gcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
| | | ||||| | | | | || ||| | | || | ||| | | | || | | |||| | ||| | | ||||| | |||| ||| | | | |||||||| |||||||||||||||||||| || | || || | | ||||| || || || || | | | ||||
gttctgtctaaaaaaccttgctctttaatgcctactacttgaagattttatttatattgcttctattttaagagttctttcctcgttcaaagttattattgctcttaagatgcattggtttcttctcagGTTGCTAGGAAGTTCACTAACAAAGTTGAAGGGAAGATGGGGTATGAGGACTTTGTCTATTTCATTCTTGCGGAAGAAGATAAATCGTCAGTGCCTAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgttttcttttgctttaccggacgttgccaacggtagcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagattgcctgcaggcaacctaatgcgcttgaattagtgttgggcgttttcttttgctttaccggacgttgccaacggtagcaccttgtgaatgatagGTTCCAAGGAGGTTTAGAAGCGGCGTTGAAGGAAAGATGGGGTATGAGGACTTCGTTTGGTTTATATTATCAGAAGAGGACAAGTCATCGGAGACCAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA