Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgaccgccgttttacactggtttctgtgacatgctgcagctactgcaagcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S87_179V6.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgtgaccgccgttttacactggtttctgtgacatg--ctgcagctactgcaagcattcgagatttaagtgttcctgaatttgt--actttgt----tgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
| |||| || | || ||||| || |||| || || | ||||| || || |||| | |||||||| || ||||||||||| |||||||||||||| || ||||| || ||||| | ||| || || | || || ||| | || |||||||
------------------gtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 15
gtgtgaccgccgttttacactggtttctgtgacatgctgcagctactgcaa--gcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
| | | ||| | | | || | || || || | | | || || || | | | | || | | | ||| | | |||||||||| | || || || || ||||||||||||||||| ||||||||||||||| || ||| || || | || || || | ||||| || |
-tatcagggcccctctgtaacatgttactttctattctaacattatttccattacaatctgccttgggttacttattatgttcaaatattttgtt-tatcagCCTTGTTTAGGTGGGGACTCCAAGACCTTGATGTTTGTGAACATCTCTCCTGATCCTTCCTCATTGGGAGAGTCGCTTTGCTCCCTACGTTTCGCAGCCA
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
---gtgtgaccgccgttttacactggtttctgtgacatgctgcagctactgcaagcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
|| | | | ||| | ||| | | || | || || | || | ||||| || ||||| | || ||| ||||||||| | || || ||||| |||||| |||||||||||||||||||||| || || | ||| || | || ||||| || || ||||| |
agcaagtttctgttctattaaa-tggcata-gaagtttgtcatatct-tagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcaagcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
ctgtttc CT-rich tract
agatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgaccgccgttttacactggtttctgtgacatgctgcagctactgcaagcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - tgctgca
- - - - - - - - - - - - - - - - - - - - - -tactgca