Sequence
atgc intronic sequence ATGC exonic sequence...tctggctcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
Basic information
species | Physcomitrella patens |
transcript | PP1S10_312V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
tctggc--tcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
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catggccttcactaccactgattag-gaattgattcttaagtcatgcaatat-tacttaatattgctcatttgtagactaatagttcatttgacatatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG
upper sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 5
--tctggctcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtt--tcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
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aaattggtaca--tggagtctacattctttt-ataatcatactgaacaagctattacaatttaatttgtttgcaccact-tgacattgtttttgtaatatctagGTACACAGCAATGAAACAAGCCTATCAGCTAGATGTCGAAGAATATATGCTCATGCTCATGACTATCATATCAATTCCATTTCAAACAACAG
upper sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 5
tctggctcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
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----------------------------------------------------gtatgctgctgctgctttttcttct-tgttgctaagcttt-gctgcagGTTTCTTGCACCGAGACAGCACCTTTTGCCAGATGTAGAAGAGTTTATGCAAATGCCCATACATATCATATAAATTCGATTTCCAATAACAG
upper sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 5
tctggctcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
| ||| || ||| | || | ||||| | ||| | | ||||| | || | |||||||| | ||| || |||||||||||||| ||||| ||||||||| | || ||||| ||||| || || || |||||
----------------------------------------------gtatgctgctgctgctgccgctttttcttct-tgttgctaagcttt-gctgcagGTTTCTTGCACCGAGACAGCACCTTTTGCCAGATGTAGAAGAGTTTATGCAAATGCCCATACATATCATATAAATTCGATTTCCAATAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
aattaac putative branch site (score: 2)
tttttgtttc putative PPT
tatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctggctcaatttgagtaattattggtttgattagggtactgcatggcatgtgtttgttgcaattaactgccaaactgcggtgctatgtttttgtttcagGTGTGGAGCGCTGAGACAGCGCTTTTGGCAAGATGTAGAAGAGTATATGCTAATGCCCATGCTTACCATATCAATTCCATCTCTAACAACAG
- - - - - - - - - - - - - - - - - - -tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca