Sequence
atgc intronic sequence ATGC exonic sequencegtacgaaagttaaatgtcctgtcatttgtcgagtttttagtgatagtcttgagtagcagttaatcctatctacttaactcgcgaccttttgtgaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
Basic information
species | Physcomitrella patens |
transcript | PP1S52_57V6.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 20
-----gtacgaaagttaaa--tgtcctgtcatttgtcgagtttttagtga-----tagtcttga----gtagcagttaatcctatc----tacttaactcgcgaccttttgtgaagttataa---gatatcaaggcacttacattgtgcc---tgtgttgtaattttggt---cagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
| | | ||| | |||| ||| |||| | |||| | || | | ||| | ||||| || | | | | | | || ||| | | ||| | | || || | | | | || ||||| | ||||| || || || || |||||||| |||||||| |||||||||||||| | |||||||| |||||||| ||||| || |||||||| | |||||
gtagaggataattgttgatgttgtcgtgtgatttttttggtttcttgtatacttctccttttggttctgctattgttaaattcattctgacatgtcattttcaaagttcctgctagtgacagttcagcatccaataagttgaataacctcatttctttggttcttttgatttgcagTTTATTGTGGTTTCCTTGAAGGAAGGCATGTTCAATAATGCAAATGTTCTTTTCCGGACAAAATTTGTGGATGGTGTTTCAACTGTTCAGCGAACTGTTG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 20
gtacgaaagttaaatgtcctgtcatttgtcgagtttttagtgatagtcttgagtagcagttaatcctatctacttaactcgcgaccttttgtgaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
| ||| | | | | | ||| | | || ||||| || | ||||| | | || | |||| | || | |||| ||||| || || || || |||||||| |||||||| |||||||||||||| | |||||||| |||||||| ||||| || |||||||| | |||||
---------------------------------tgtttggcgtatacttctctttgagtttattttcaaaattcctgctagcgacagttcagcacccaataag---ttgaataacct-catt-------tcttttgatttg---cagTTTATTGTGGTTTCCTTGAAGGAAGGCATGTTCAATAATGCAAATGTTCTTTTCCGGACAAAATTTGTGGATGGTGTTTCAACTGTTCAGCGAACTGTTG
upper sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 19
gtacgaaagttaaatgtcctgtcatttgtcgagtttttagtgatagtcttgagtagcagttaatcctatctacttaactcgcgaccttttgtgaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
| | | | | |||||| | | || | |||| | || |||| | |||||||||||| || || ||||| ||||| |||||||| || ||||| || |||||||| || || || || |||||||| ||||| || |||||||| |
-----------------------------------------------------------------------------gtattggcttgtgctgaagtcacattctact-------tcacatc-tatctcccttgt-----tcctcagTTCATCGTGGTCTCTTTGAAAGAGGGGATGTTTAACAACGCAAACGTTATCTTCCGTACTAAGTTCGTGGATGGAGTGTCAACCGTAACAAGGACAGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
cacttac putative branch site (score: 2)
tataagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaaagttaaatgtcctgtcatttgtcgagtttttagtgatagtcttgagtagcagttaatcctatctacttaactcgcgaccttttgtgaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcagTTCATCGTAGTGTCGTTGAAGGAGGGCATGTTTAATAATGCAAATGTCATCTTCCGGACCAAATTTGTCGATGGAGTCTCAACTGTCACAAGGACTGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA