Sequence
atgc intronic sequence ATGC exonic sequence...atactaggttgggcagatggtagaatacttttcttttctaggttttgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
Basic information
species | Physcomitrella patens |
transcript | PP1S47_172V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_172V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------atactaggttgg-gcagatggtagaatacttttcttttctaggtt-----ttgttgccgatga---aaactag--caaagaaagtg-actgatgactgt---tattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
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gtaagttcaacatatttttctctcatcatttcaggaattactttttgtatttcgacacttattacatcgacgcccataaccttctacttttgctcttaatgctgtaattctatgtcaattatttggattactttaaataagctgcagtgacaattgtggttcttcattttcagAGTTTTTCCAGAACAAGTTAGTAGAGACCATACAGTTCATGGAAGTTCTTAACTTAAAGGACAGTGTTGAGAAAGATAGCTTTTTCCGTAAACTACCGAA
upper sequence: PP1S47_172V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
atactaggttgggcagatggtagaatac-ttttcttttctaggttttgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
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gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctctt-gattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
upper sequence: PP1S47_172V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 8
--atactaggttgggcagatggtagaatacttttcttttctaggttttgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
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atttctttgcctcagtctctttcttcttagtattcccttctttcttccttttcctttttttttttg-gtgcctactaatttcagaa-gatatgcattggcagAATATTTCCAAAATAAGTTAGTGGATACTATACATTTCATGGACATTCTTAATTTGAAGGACAGTGTTGAAAAGGATACCTTCTTCCGTAAGCTTCCAAAMapped 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|162171348|gb|FC346441.1|FC346441EST: TTCTGCTCCTGTGAAAAGATTGAACTCAGCTAAATTATTAGAAAATAGTG AGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGA
genomic: TTCTGCTCCTGTGAAAAGATTGAACTCAGCTAAATTATTAGAAAATAGTGgtgagtctac ... tgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
tattgac putative branch site (score: 2)
atgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atactaggttgggcagatggtagaatacttttcttttctaggttttgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT