Sequence
atgc intronic sequence ATGC exonic sequence...taattgcacagttgcaactcctcaaacgagctcctgcaccgtcatcgctgatatctcagatttttttttttttaaatcaccctcgtcattgtgtcaatagGTAGCATCAGCGATTACAGTGTGGACTCGACTTCAACCCGATTATGCATCGAATATGTGGAATGAAGCTCTTAACAAGCGCTTGGGTACTAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S307_69V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S307_69V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ34102 (Selaginella moellendorffii), 3'ss of exon 4
taattgcacagttgcaactcctcaaacgagctcctgcaccgtcatcgctgatatctcagatttttttttttttaaatcaccctcgtcattgtgtcaatagGTAGCATCAGCGATTACAGTGTGGACTCGACTTCAACCCGATTATGCATCGAATATGTGGAATGAAGCTCTTAACAAGCGCTTGGGTACTAAG
| ||| | || | || || | || | ||| | |||||| || || | | | || || ||||||||||| ||||| || ||||| | |||||||||||||||||||| |||||||| | | ||| ||
--------------------------------------gtaagagagctttagtttcctttccaaagcttgttgatacatgttttcggttggg---atagGTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAG
upper sequence: PP1S307_69V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ12449 (Selaginella moellendorffii), 3'ss of exon 4
taattgcacagttgcaactcctcaaacgagctcctgcaccgtcatcgctgatatctcagatttttttttttttaaatcaccctcgtcattgtgtcaatagGTAGCATCAGCGATTACAGTGTGGACTCGACTTCAACCCGATTATGCATCGAATATGTGGAATGAAGCTCTTAACAAGCGCTTGGGTACTAAG
| || | | | || || | || || ||| | |||||| || || | | | || || ||||||||||| ||||| || ||||| | |||||||||||||||||||| |||||||| | | ||| ||
-------------------------------------------gtaagagagctttagtttccaaagcttgttgacacattttctcggttggg---atagGTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctgatatctcagatttttttttttttaaatcaccctcgtcattgtgtcaatagGTAGCATCAGCGATTACAGTGTGGACTCGACTTCAACCCGATTATGCATCGAATATGTGGAATGAAGCTCTTAACAAGCGCTTGGGTACTAAG
cgctgat putative branch site (score: 4)
atatctcagatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattgcacagttgcaactcctcaaacgagctcctgcaccgtcatcgctgatatctcagatttttttttttttaaatcaccctcgtcattgtgtcaatagGTAGCATCAGCGATTACAGTGTGGACTCGACTTCAACCCGATTATGCATCGAATATGTGGAATGAAGCTCTTAACAAGCGCTTGGGTACTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- -ttgcaca
- - - - - - - - - - - - - - - -tcctgca