Sequence
atgc intronic sequence ATGC exonic sequencegtcagtctcggatcttgatccccatttgtgtgtattcctctggatgcttctctgtgggtacgcgagtcatcttcccaatagacaggccttagcctctcttttgcttgtctttcttctctggcttctctcacctcttttcctccttccttcttcccatgttggggaaacgttggacttgtctctgctttgctattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTG
Basic information
species | Physcomitrella patens |
transcript | PP1S48_128V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S48_128V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 4
gtcagtctcggatcttgatccccatttgtgtgtattcctctggatgcttctctgtgggtacgcgagtcatcttcccaatagacaggccttagcctctcttttgcttgtctttcttctctggcttctctcacctcttttcctccttccttcttcccatgttggggaaacgttggacttgtctctgctttgctattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTG---------
| ||| | |||||| || ||| || ||| |||| ||| || ||| | | | |||| | | | ||| | || | ||| ||||||||||| ||| |||| || || ||| ||| || ||||| || ||||| |||||||| ||||||||||| |||||||| ||||
---------------------------------------------------------------------------------------------------agttctttctccttttctctatctgttcttctctatttattctcttctctctctcc-tgt--------ctctatgccggtctaccgtcgggcactctctggacac-acagCCTAATCGAATTCTCTTAGTTACAATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGA
upper sequence: PP1S48_128V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ25472 (Selaginella moellendorffii), 3'ss of exon 4
gtcagtctcggatcttgatccccatttgtgtgtattcctctggatgcttctctgtgggtacgcgagtcatcttcccaatagacaggccttagcctctcttttgcttgtctttcttctctggcttctctcacctcttttcctccttccttcttcccatgttggggaaacgttggacttgtctctgctttgctattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTG
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gtttgtctcctaggatggac----tgagtgcctttatctctagatggaagcaccagttctcaagaatttttctttctttctttttgctttggattttctttagctttctacttcagtactggctccctcacttctttttctcttcctgtcttctcttgt----atcttgctggaa----cgcggtgtgggtcttcttcagGATCAACAACCCAACCGAATTCTCTTAGTTACTATTCACCACCCGCTCTATCCCATCACCGTGGATGTGCTGCATCAAGTTTTTAACCCTCATGGCCATGMapped 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|100444485|gb|BY964183.1|BY964183EST: TCACTACTCCCGATCAAAATGGACAAACAAGGCGGTTACCTGCAGAGCAG GAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTAT
genomic: TCACTACTCCCGATCAAAATGGACAAACAAGGCGGTTACCTGCAGAGCAGgtcagtctcg ... tattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttcttcccatgttggggaaacgttggacttgtctctgctttgctattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTG
ctttgctattcttc CT-rich tract
tattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtctcggatcttgatccccatttgtgtgtattcctctggatgcttctctgtgggtacgcgagtcatcttcccaatagacaggccttagcctctcttttgcttgtctttcttctctggcttctctcacctcttttcctccttccttcttcccatgttggggaaacgttggacttgtctctgctttgctattcttcagGAACTGCTGCCCAATCGAATTCTTTTAATTACCATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC