Sequence
atgc intronic sequence ATGC exonic sequence...atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggtgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
Basic information
species | Physcomitrella patens |
transcript | PP1S29_139V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G32600.1 (Arabidopsis thaliana), 3'ss of exon 1
-----atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggtgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
| ||| || | |||| || | || || | | | || | || | | || || || | | ||| || ||| | |||||| ||||| ||||| || || | ||||| |||||||| || || || || ||||| ||||| ||||| ||| ||||||||||||| |||||||| | ||
cttgagtttgtttggctgttgtttctagaattaggttcttttttttaatt--ttcccctcatgccactaattt---gatttttggtgtgtttttatgttgtgcagCTATGAGTGTAAACTATGTCTAACACTGCATAACAATGAAGGAAACTACTTGGCACATACTCAAGGTAAGAGGCATCAGACAAACTTGGCAAAGAGAGCT
upper sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
atgtgtacggatattgtccctttctctttgtactgcatggaaggtc-atttcactggaacgatt-atcttattgaaatatagtgggtatttccttgg-----tgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
| || | | |||| | | | | |||| ||| | | || || || || || || ||| || | | ||| | |||| | ||| ||||| |||||||||||| ||||| | || ||||||||||| ||||||||||| || || ||||| ||| |||||||||| |||||||| || | ||
-------cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
upper sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggt----gcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
| ||| | | | |||||||| | | ||| | ||| || || |||| | ||| | | | ||| | ||||| |||| || || ||||||||||||||||| || || ||||| ||||| || || ||||| || || ||||||||||| || ||||| |||||||| || || ||
gtctgtctctctttcatttttttctcttggaggagaatgtccg-ctgtttttctcga--gattgggcgagtga--tggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
upper sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ08420 (Selaginella moellendorffii), 3'ss of exon 1
atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggt----gcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
| ||| | | | |||||||| | | ||| | ||| || || |||| | ||| | | | ||| | ||||| |||| || || ||||||||||||||||| || || ||||| ||||| || || ||||| || || ||||||||||| || ||||| |||||||| || || ||
gtatgtctctctttcatgtttttctcttggaggagaatgtccg-ctgtttttctcga--gattgggcgagtga--tggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGGAACTACTTGGCACACACGCAAGGCAAGCGACACCAGACGAATTTGGCCAAGCGCGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttcactggaacgattatcttattgaaatatagtgggtatttccttggtgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
tatttcctt CT-rich tract
attatcttattgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggtgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA
- - - - - - - - - - - - - - - tactgca