Sequence
atgc intronic sequence ATGC exonic sequencegtgagacgattcccagttgacgggtgctgtctgctggcgaaattctcttctttgtggagcagctcattgtacaacactgtttgttattgaccatcatcgatctgtgttgtttcttgagtttgaatctttcgattcgtatattcacaggttctttgccaaatttcccacattgcagtctaataatttttggtttgcagTCGAAGCCGGCTCTTCCCGCCTTGGAGCGCCTCATCCACTCTAACGACGAAGAGGTCCTCACTGATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGA
Basic information
species | Physcomitrella patens |
transcript | PP1S63_171V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 5
gtgagacgattcccagttgacgggtgctgtctgctggcgaaattctcttctttgtggagcagctcattgtacaacactgtttgttattgaccatcatcgatctgtgttgtttcttgagtttgaatctttcgattcgtatattcacaggttctttgccaaatttcccacattgcagt----ctaataatttttggttt----gcagTCGAAGCCGGCTCTTCCCGCCTTGGAGCGCCTCATCCACTCTAACGACGAAGAGGTCCTCACTGATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGA
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---------------------------------------------------------------------------------------------------------------------gtttaattctgggctaccttctactttgatgcactgacctaagtttttatcattaggatggttttgttgattttttgtgttcgagcagGTCAAACCAGCGCTTTCTGCACTGCAGCGCCTCATCCATTCTCAGGACGAGGAGGTCCTGACTGATGCCTGCTGGGCTCTTTCTTATTTGTCTGATGGAA
upper sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 5
gtgagacgattcccagttgacgggtgctgtctgctggcgaaattctcttctttgtggagcagctcattgtacaacactgtttgttattgaccatcatcgatctgtgttgtttcttgagtttgaatctttcgattcgtatattcacaggttctttgccaaatttcccacattgcagtctaataatttttggtttgcagTCGAAGCCGGCTCTTCCCGCCTTGGAGCGCCTCATCCACTCTAACGACGAAGAGGTCCTCACTGATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGA
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----------------------------------------------------------------------------------------------------------------------------gtatgtgggtcatttgtaggcatgtcgata--caaatttg----atcgttggtcggtgttgttt--cttgcagTCGAGACCTGCTTTATCTGCTCTAGAAAAGCTGATTCATTCGACTGACGAAGAAGTCCTTACTGATGCATGCTGGGCTTTGTCATACATATCCGATGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacaggttctttgccaaatttcccacattgcagtctaataatttttggtttgcagTCGAAGCCGGCTCTTCCCGCCTTGGAGCGCCTCATCCACTCTAACGACGAAGAGGTCCTCACTGATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGA
gtctaat putative branch site (score: 3)
ttttt putative PPT
taataatttttggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagacgattcccagttgacgggtgctgtctgctggcgaaattctcttctttgtggagcagctcattgtacaacactgtttgttattgaccatcatcgatctgtgttgtttcttgagtttgaatctttcgattcgtatattcacaggttctttgccaaatttcccacattgcagtctaataatttttggtttgcagTCGAAGCCGGCTCTTCCCGCCTTGGAGCGCCTCATCCACTCTAACGACGAAGAGGTCCTCACTGATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG