Sequence
atgc intronic sequence ATGC exonic sequencegtatttcgcactcttctccttctttgattgcatcctcaataggttcaagggggttttactctcagctgtattacaatgtgcgggttacgccttcgtcgttttggtttaggactttagaggttggtgggtttgtggagtaattgaatactgaaatagagttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC
Basic information
species | Physcomitrella patens |
transcript | PP1S51_233V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S51_233V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
gtatttcgcactcttctccttctttgattgcatcctcaataggttcaagggggttttactctcagctgtattacaatgtgcgggttacgccttcgtcgttttggtttaggactttagaggttggtgggtttgtggagtaattgaatactgaaatag--agttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC
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---------------------------------------------------------------------------atatttgcattgtgagtactttgaaat--tttctgattttgcaa-----tatctctgtctatta-ctatatacttcggtagtcagtttcaagcaattc-ctatttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG---------------
upper sequence: PP1S51_233V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 6
gtatttcgcactcttctccttctttgattgcatcctcaataggttcaagggggttttactctcagctgtattacaatgtgcgggttacgccttcgtcgttttggtttaggactt--tagaggttggtgggtttgtggagtaattgaatactgaaatagagttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC
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----------------------------------------------------------------------------------ggtt-cagagtcactattatg-ttgagcatttggtatattctcatgcacttatccctgtacaaagacatgcctctcagttttaactggatcctgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG---------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162166717|gb|FC342686.1|FC342686EST: TAACGCCCTGGAAGGGGATTTTGCTCTTTGGTCCTCCGGGAACTGGGAAG ACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAAC
genomic: TAACGCCCTGGAAGGGGATTTTGCTCTTTGGTCCTCCGGGAACTGGGAAGgtatttcgca ... caactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtggagtaattgaatactgaaatagagttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC
tgctcac putative branch site (score: 2)
taattgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcgcactcttctccttctttgattgcatcctcaataggttcaagggggttttactctcagctgtattacaatgtgcgggttacgccttcgtcgttttggtttaggactttagaggttggtgggtttgtggagtaattgaatactgaaatagagttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC