Sequence
atgc intronic sequence ATGC exonic sequence...attctcaaaaggaggaatccatgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggctgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
Basic information
species | Physcomitrella patens |
transcript | PP1S97_167V6.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
---at-tctcaaaaggaggaatccatgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggctgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
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ccaatgtttcttggctacgatttatttcgattatataacttccatgaaaa-aatttccagaaaacgattgatatgcttctgaatta-ttgtttac--attgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 2
---attctcaaaaggaggaatcc-----atgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggctgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
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cgaactttcctggtcctggattcttttaattagatagcatggaagaaaggatcttgaca---aaaagacctagaa-----tcttaaggttttgacgttttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
attctcaaaaggaggaatccatgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggc-tgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
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gtggttattggtattgtacaatatgatt-tatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGGMapped 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|100354113|gb|BY945717.1|BY945717EST: ATGTTGAAGAATTTTATCGGCAGTGTGATCCAG AGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGA
genomic: ATGTTGAAGAATTTTATCGGCAGTGTGATCCAGgtgagaaatc ... ttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatatgcagtggttcgcgaagtgactccttaattggctgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
tcttaat putative branch site (score: 3)
ctgcttctt CT-rich tract
ttcttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attctcaaaaggaggaatccatgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggctgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG