Sequence
atgc intronic sequence ATGC exonic sequencegttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S245_17V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagtttt-ttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
|| ||| | |||| || |||||| | | | | | | | || | | | || | | || | || | | || || ||||||| || ||||||||||| || ||||||||||| ||||| | | || ||||||||||||||||| ||||| ||| | |||||||||||||||||||| |
----------------------ttcaaaacaatg-tgcatatatacacagcactatagaacgtcatagctcctataccttgtgatcatgcaacttt----attcactttctctttcatcatc-ttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG
upper sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttc--tcttaatgtttaataatctttgtgctgt-cattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
|||| | || | || | || || | ||||| | |||| || | || ||||||| | || |||||||| ||||| ||||| || ||||||||| | | || ||| | ||||| || || || ||||||||||| ||| | ||||||||||||||||| ||||
------------------------------gcaaatgcagagcaatttgtttgtcaatgttgttaacttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG
upper sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 8
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
| ||| |||| | || | |||| | | || | || | | | | || | || || | ||||||||||||||| || || || ||||||||||| ||||| || | ||||| || |||||||| || ||||| ||| | ||||| ||||| |||||||| |
--------------------------------------------gtaaagtgttttctatttctctacttctatcttgttctctctacattttgcctctctcttatgtttttggttaatacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACACGTGACACAAGAAGACTTTGAGATGGCGGTGGCCAAGGTAATGAAGAAAG
upper sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
| ||| | || | ||| | | || | | | | ||||| | |||| | || || | | ||||||||| ||||| || || ||||||||||| || ||||| || | |||||||| || || || || ||||| ||| ||||||||||||| |||||||| |
--------------------------------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctc----tctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
upper sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 8
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgttta-ataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
| |||| || || | ||| || | | || || | |||| | |||| | | | | || || |||| ||||| || | ||||| || ||||||||||| || |||||||||||| | || || | |||||||| |||||||| |||||||| ||| | ||||| ||||||||||| ||||
---------actaagtccttattcttcatcat-------atcaagtgcggtcggttatctgttttgtcttctaacat---caagcatgtctaactaaacttttatataattgtt---------tgcagGCGGTATGCACAGAAGCTGGAATGTTTGCTCTAAGGGAGAGGAGAGTACATGTGACACAAGAAGATTTTGAGATGGCAGTGGCAAAGGTGATGAAAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
tttgtttttctcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcctactaaagagtcgttgttttgtcacatttctgcaattagacacagttttttgtgctttttcttttcttttctatttgtttgtttttctcttaatgtttaataatctttgtgctgtcattcagGCTGTGTGCACAGAAGCAGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTAACACAAGAGGATTTTGAAATGTCTGTGGCGAAGGTGATGAAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG