Sequence
atgc intronic sequence ATGC exonic sequence...caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
Basic information
species | Physcomitrella patens |
transcript | PP1S35_125V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ29447 (Selaginella moellendorffii), 3'ss of exon 1
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
|| || || ||| | | | || ||| | | | | || | || || ||| || | | || |||| || ||||| | || ||||||||||| || || || || || ||||||||||| |||||||| |||||| | |||||||| || || || |||||| |
-----gtctc-caaggcaaatcccgcaaaacccacgatcaaacttgtcaagttcttc-----gcttgaatctgtgcttgctttttcctgtgtgc---cagGTTTCCAGATCTCCCACTCCATGGGAGGCGGGACTGGTTCGGGGATGGGGACGCTGCTCATCTCCAAGATTCGCGAGGAATACCCCGACCGGATGATGCT
upper sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ28017 (Selaginella moellendorffii), 3'ss of exon 1
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
|| || || ||| | | | || ||| | | | | || | | || || | | | | ||| | | | |||| || ||||| | || |||||||||||||| || || || || ||||||||||| |||||||| |||||| | |||||||| || || || |||||| |
-----gtctc-caaggcaaatcccgcaaaacccatgatcaaacttgtcaagttcttc---gcttgaatctgtgcttgcttgctttttcctgtgtgc-cagGTTTCCAGATCTCCCACTCCATGGGAGGTGGGACTGGTTCGGGGATGGGGACGCTGCTCATCTCCAAGATTCGCGAGGAATACCCCGACCGAATGATGCT
upper sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ34212 (Selaginella moellendorffii), 3'ss of exon 1
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
|||| | | ||||||| | ||| | || ||| | | | || | | | | ||| ||| | |||||||||| | ||||| ||||||||||| || |||||||| |||||||| ||||| |||||||| ||||| || || || || ||||| | |||||| |
tctttgtttttccacctggtgtttttatgttctagtttctcgatctaagttgcaactctttcaaggatctaacacgaggatggttttatttgttggtcagGATTTCAAGTGTGTCACTCCATGGGAGGAGGCACGGGATCTGGCATGGGAACGCTCCTCATCTCCAAGATAAGAGAAGAGTACCCGGACAGAATGATGCT
upper sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ07091 (Selaginella moellendorffii), 3'ss of exon 1
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
| || || | || | || | | | || ||| | | | | || ||| |||| || ||||| | || ||||||||||| || ||||| || || ||||||||||| |||||||| ||||| | ||||||||||| || ||||||||| |
--------------------------gtctccaaggcaaagcacaaaacccatggtcaaacttgc-ggattctttgcttaactctgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACGGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATATCCCGACCGCATGATGCT
upper sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ05935 (Selaginella moellendorffii), 3'ss of exon 1
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaa-cagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
| || || | || | ||| | | | || ||| | | | || | ||| |||| || ||||| | || ||||||||||| || || || || || ||||||||||| |||||||| ||||| | |||||||| || || ||||||||| |
--------------------------gtctccaaggcaaagcacaaaacccatgatcaaacttgc-ggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
gtttgat putative branch site (score: 5)
atactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaacagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA