Sequence
atgc intronic sequence ATGC exonic sequencegtgagaaattcgtctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
Basic information
species | Physcomitrella patens |
transcript | PP1S140_64V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gtgagaaattcgtctcataaccgttctgctcatcatg-tgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
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----------------------gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatga----tacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
upper sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
gtgagaaattcgtctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
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---------------------------gtaattctttttcgaaatc---cttgcttgtcttctcccatgatacggttttttttacttgtttttgccttattatttt---cagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC
upper sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtgagaaattcgt-ctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
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gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggcc-ttgaccgcatcctgggctgtcc--ttgctttgctggtggcg----acgtgc------agGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCCMapped 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|162193436|gb|FC370989.1|FC370989EST: AGATAGACAATGGGCAAGAAGTTGTCTTTACATATGATGTAGCTTTTAAG TACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACA
genomic: AGATAGACAATGGGCAAGAAGTTGTCTTTACATATGATGTAGCTTTTAAGgtgagaaatt ... gcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACA
EST:
gi|162151385|gb|FC327514.1|FC327514EST: AGATAGACAATGGGCAAGAAGTTGTCTTTACATATGATGTAGCTTTTAAG TACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACA
genomic: AGATAGACAATGGGCAAGAAGTTGTCTTTACATATGATGTAGCTTTTAAGgtgagaaatt ... gcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
aatctattttctaaca 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaaattcgtctcataaccgttctgctcatcatgtgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT