Sequence
atgc intronic sequence ATGC exonic sequence...tatgagtgccaccctggcagccgtggtgcgtcggtgatgctcgattggttggggattcgacggtgagtgcagggtattgacgaatgcggtttgtgtgcagCTGGTGGACAAGGACCCCGACCGTGCGATCGCGTTGTTTTGGGCAGCCATAAACGCTGGGGACAGAGTTGACAGCGCTCTGAAGGACATGGCCATAGTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S8_159V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S8_159V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 1
tatgagtgccaccctggcagccgtggtgcgtcggtgatgctcgattggttggggattcgacggtgagtgcagggtattgacgaatgcggtttgtgtgcagCTGGTGGACAAGGACCCCGACCGTGCGATCGCGTTGTTTTGGGCAGCCATAAACGCTGGGGACAGAGTTGACAGCGCTCTGAAGGACATGGCCATAGTGA
|||| | | | || || ||| | | || || || | || || || || | | | || | |||||||||||||||||| || || ||||||||| |||| ||||| || || ||||| || ||| | || |||||||| || |||||||||||||| ||||
------------------gtacgtgat-tgcgagcga-gcgttcttgatggtggtttggattgggattgggttgtgatggtggtggtgattcg---gcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGGCGGCGATCAACGCCGGCGACCGGGTGGACAGCGCGCTCAAGGACATGGCCATCGTGA
upper sequence: PP1S8_159V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G079613_T01 (Zea mays), 3'ss of exon 1
-tatgagtgccaccctggcagccgtggtgcgtcggtgatgctcgattggttggggattcgacggtgagtgcagggtattgacgaatgcggtttgtgtgcagCTGGTGGACAAGGACCCCGACCGTGCGATCGCGTTGTTTTGGGCAGCCATAAACGCTGGGGACAGAGTTGACAGCGCTCTGAAGGACATGGCCATAGTGA
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gaagaaacatttgaatcatgacccctat-cttcatcgctgcttttttagagttttcttaagcctaatttgtatagtatttttttcattgcatgagaaccagCTCGTGGAGAAGCAACCGGATGTGGCGATCGTGTGGTTCTGGAAGGCAATCAACTCAGGGGACAGGGTGGACAGCGCCCTGAAGGACATGGCCATGGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttggggattcgacggtgagtgcagggtattgacgaatgcggtttgtgtgcagCTGGTGGACAAGGACCCCGACCGTGCGATCGCGTTGTTTTGGGCAGCCATAAACGCTGGGGACAGAGTTGACAGCGCTCTGAAGGACATGGCCATAGTGA
tattgac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgagtgccaccctggcagccgtggtgcgtcggtgatgctcgattggttggggattcgacggtgagtgcagggtattgacgaatgcggtttgtgtgcagCTGGTGGACAAGGACCCCGACCGTGCGATCGCGTTGTTTTGGGCAGCCATAAACGCTGGGGACAGAGTTGACAGCGCTCTGAAGGACATGGCCATAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG