Sequence
atgc intronic sequence ATGC exonic sequencegtacgtttctttacgcaatggttgttgaactcttcaacaaaatatttcagcggccacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
Basic information
species | Physcomitrella patens |
transcript | PP1S174_62V6.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S174_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 2
gtacgtttctttacgcaatggttgttgaac-tcttcaacaaaatatttcagcggccacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
||| || | ||| | || ||| | | | | | || || | || | |||| | || | || | ||| | | ||||| |||||||| || |||||||||||||||||||| | | | | || || |||| |||| | |||||| ||||| |||||||
gtaagtaagcgaa-gcactagtcgttcgtcgccattgatgagatgagatga--gctttgcattcgagttctg--ggctgc--gattctg-attcgggtatgagcgaacagGATGCAGGTGGAGGTGAGCAAGTACACGGAGGGGCTCAGCGACAAGCGGATGCGGCCGAACGAGTTGCCGGTGTCGCTCATCCGCTACGACG
upper sequence: PP1S174_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 2
-gtacgtttctttacgcaatggttgttg-aactcttcaacaaaatatttcagcggccacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
| | | | | |||| ||| || | | ||||| | | | | || | |||| |||| || |||||| || | | ||| |||||||||||||||||||||||||||| || || || | || | ||| ||| || || || | || |||| | || |
ataaaggctgtatcttgaatgtgagttctaagtatctaacaatttttagtattagtaaca--gctgaaatatgcttactgcttaat-acatctat--------tactacagAATGCAGGTTGAAGTGAGCAAGTATACAGAAGGCGTGAATGAAAAGGCATTACGACCAAATGGATTACCTAAGTCATTAATTC---------
upper sequence: PP1S174_62V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G33560.1 (Glycine max), 3'ss of exon 2
gtacgtttctttacgcaatggttgttgaactcttcaacaaaatatttcagcggccacgaggtccaa-atctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
|| ||| | || || | || | || || | | | || | | | ||||||| || ||| ||| |||||||||||||||| |||||||||||||| || || || | ||| ||| || || || | || | || | || ||||| || |
acacaaactcttaag-----attaacaaagct---agaaatgtgctttcatggagaaaggttgtaacagattaaatttgcttaatgcttaatacagttat--tactacagAATGCAGGTTGAGGTGAGCAAGTACACAGAAGGCATGAATGAAAAGGCATTACGACCAAATGGATTACCTAAATCATTAATTCGTTATGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
acttaat putative branch site (score: 4)
tacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtttctttacgcaatggttgttgaactcttcaacaaaatatttcagcggccacgaggtccaaatctgctgcctacttaatgacgtgcacggttgcggtacaacagAATGCAGGTTGAAGTGAGCAAGTACACGGAGGGTGCTAAAGCCGTGGCTCGACGTCCCAACGGCCTGCCCGAGTCGCTGATCCGTTACGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT