Sequence
atgc intronic sequence ATGC exonic sequence...gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagccctgaacaatttatgcttgaacaccgaatgaagtttgtttgcagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
Basic information
species | Physcomitrella patens |
transcript | PP1S8_277V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S8_277V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv04s0023g03720.t01 (Vitis vinifera), 3'ss of exon 1
------gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagcc-ctgaacaatttatgcttgaacaccgaatgaagtttgtttg--cagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
| | | ||| || | || | | | ||| | || | ||| | | | || | | |||| |||||| ||| | || |||||||| || || ||||| | || |||||| || |||||| | ||||||||||| |||||||| |||||||||||||| || || |
gtaagcttccgttctgggaaatcttgaaatttgccaacaaaccgaggtttcttcttttgcgtgattgatctctgtttgatgggttggattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATTCCGCTATTTTGGTCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
upper sequence: PP1S8_277V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv04s0023g03740.t01 (Vitis vinifera), 3'ss of exon 1
------gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagccctgaacaatttatgcttga--acaccga--atgaagtttgtttg--cagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
| | | ||| || | || | | | ||| | || | ||| || | || |||| || |||| |||||| ||| | || |||||||| || || ||||| | || ||||||| || |||||| | ||||||||||| |||||||| |||||||||||||| || || |
gtaagcttccgttctgggtaatcttgaaatttgccaacaaaccgaggtttcttcttttgcg---tgattgatctctgtttgatgggtttgattatgacttttgttgcatcagTTGGTTGACAAGGACCCGGAAAAGGCAATCCCGCTATTTTGGGCCGCCATTAATGCTGGAGATCGAGTGGATAGTGCGCTCAAGGACATGGCCATTGTGA
upper sequence: PP1S8_277V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0005g05680.t01 (Vitis vinifera), 3'ss of exon 1
gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagccctgaacaatttatgcttgaacaccgaatgaagtttgtttg-cagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
|| | || || || | | || || | | || || ||| ||| | | | || | ||||| || || |||||||| || ||| |||| | | |||||| | ||||| ||| |||||||| |||| |||||||| || |||||||||||| | || |
-caaattaacttgacatgcatcatttgttcgttatctagcgaaagcaatatgtgttatggattaatatatacaattttgttttgttttcatggtaggacagCTGGTTGAGAAGGATCCTGAAGTAGCTATAGTATTGTTTTGGAAGGCAATAAATGCAGGAGATAGAGTAGATAGTGCGCTTAAGGACATGGCAGTAGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataattaagccctgaacaatttatgcttgaacaccgaatgaagtttgtttgcagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
tttgttt CT-rich tract
aacaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatcacaaagaattgtggatttagaggatgatagagaatttgtataattaagccctgaacaatttatgcttgaacaccgaatgaagtttgtttgcagCTTGTCGACAAGGATCCCGATCGAGCAATAGCACTTTTTTGGGAAGCAATTAATTCAGGAGATCGAGTTGATAGTGCTCTCAAGGACATGGCAATCGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaca