Sequence
atgc intronic sequence ATGC exonic sequence...gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
Basic information
species | Physcomitrella patens |
transcript | PP1S104_2V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaattt-cgatttccgactt-acgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
|||| | | ||| || || | | | ||| | || ||| | | | | | || | |||| || | ||||| ||||| || ||| | || |||||||| ||||||||||||||||| || ||||| ||||| || | || || || |||| || |
-----------------------gttggacattt--attt--ttgttatatgtaagataataaatagtgtttcatcaatgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 8
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttg----tgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT--------------------------------------------------------------------------------------------
| | | | ||| || || |||| || |||| || | | | | ||| || || | || || | | |||| || | |||||||| || |||||| | | |||||||| ||||| |||||||||||||| || |||||||| ||| | || || ||| | ||||| |
----gtttgacatctgtaaggtctttccttttatgtattcggt-gttgtttttcgagtagtgtaactctgactgaattatgcttgtaaattttgattca---agggaactgttgtggagggcacaatacaacaattatttgaagggcatcacatgaattatatcgagtgtatcaatgtggatatgaaatcaactagAAAGGAATCCTTCTATGGCAAGTGATTGTGTTATCGCATCATGGTCATTATGTCCAAACATGCCCCTTTGACCTGATTGGTGTACACTCCAATGCAGATC
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
|| | | | | | | || | ||| | | | |||| ||| | | | ||| ||| | ||| ||||| || | || ||||| || ||||| || || |||||||| |||||||||||||||||||||||||||||||| || | ||| || ||| | |||||||
--gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgattatg----ttcatttt--gtctt---tagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattg--tgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
|| | | | | || |||| || | || || | | | || |||| ||| | | || | |||| | ||| ||||| || | || ||||| || ||||| || | |||||||| ||||||||||| |||||||||||||||||||| || | ||| || ||| | |||||||
--gtaaaggatgatctt-tggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgatt-----atgttaatttt-gtctt---tagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
| | | | | | | | || || || | || || | | | | | | || || | || ||| || | || ||||| || |||||||| | |||||||| || ||||||||||| || |||||||||||||| || | || || ||| | |||||||
---------gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttg----ttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
| | | ||| | | || ||||| | ||||| | | | | | | | || | | | | ||| |||| || | || ||||| || |||||||| | |||||||| || ||||||||||| || |||||||||||||| || | || || ||| | |||||||
---------gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgtt-ttgtgttatttgtctt---cagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
| | | | ||||||| | | || | | | | || || | || ||| ||| || |||||| || | |||||||| || |||||| | |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||| || || ||||| || |
---------gtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctc----ttttttcttcgtttttctgtagGGAACTGTTGTGGAGGGAACAATACAACAACTTTTTGAGGGCCACCATATGAATTACATTGAGTGCATAAATGTAGATTTTAAATCTACACGGAAAGAAT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
||| || || | | | | | | | || | | ||| ||| || | || || || || || || ||||| | ||||| ||||||||||||||||||||||| |||||||||||||| || | |||||||||||| ||||| |
----------------------------------------gtttactgctattttcttcacgt-taaatgttttctaacaccaagctcc-act---acagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 6
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
|||| | | |||| | | | || || || | | ||| | | |||| | |||| || || || || || ||||| ||| | |||||||| || ||||||||||| || |||||||||||||| ||||||| || || || ||||| ||||
--------------------------------gtgagtact----ttgtacgt---tgaacttcaaagctattcttatcttctactc---actt-ctcagGGAACCGCTGTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGT
upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
||| || || | | | | | | | || | | ||| ||| || | || || || || || || ||||| | ||||| |||||||| |||||||||||||| |||||||||||||| || | ||||||||||| ||||| |
----------------------------------------gtttactgctattttcttcacgt-taaatgttttctaacaccaagctcc-act---acagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
gacttac putative branch site (score: 2)
taaaatttcgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG