Sequence
atgc intronic sequence ATGC exonic sequenceTACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgctgtcttcaattcccttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca...
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G049088_T02 (Zea mays), 5'ss of exon 1
TACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgctgtcttcaattcccttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca
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CGCTGTCTAGCGCCACCAAGCAGAAGGTGGCGGCGGCGAAGCAGTACATCGAGAACCACTACAAGTCGCAGATGAAGTCGCTTCAGGAGCGCAAGGAGAGgtcagtccactccactccactccactccactccactttccttcctggtgtgatggcaatgcgcgtgtgcctgggtgatttgagggggctcagtgctggca
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 5'ss of exon 1
TACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgctgtcttcaattcccttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca--------
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CACCTTCAAATGTCACAAAGCAGAAAGTTGCAGCTGCAAAGCAGTATATTGAGAACCATTACAAGGAGCAAATGAAGAGTCTTCAGGAGAGGAGGGAACGgtatgacaatactcttaaagataaatttg---aaattttaggcacataatatctgtccctgagttagcttaca-----cttctatagaatacacgaactacaggggat
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 5'ss of exon 1
TACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgctgtcttcaattccc-----ttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca
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CGCCCTCAAATGTGACCAAGCAGAAGGTTGCAGCTGCAAAGCAGTATATAGAAAACCATTATAAGGAGCAGATGAAGAATCTTCAGGAGAGGAAGGAGCGgtatggcttccattcttcatctataaatgtacttggtagaatttgttgcttttttcc-ccacatttattttggtca-gaagatgtgatacagtatctttgat---
upper sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ16108 (Selaginella moellendorffii), 5'ss of exon 1
TACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAAC-----TACGgtattcatgctgtcttcaattcccttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca
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CCCCATCGAATGTTACCAAGCAAAAGGTCGCGGCTGCCAAGCAGTACATCGAGAACCACTACAAATCGCAATTGAAGAATCTCGAGGAACGTAAGGAGAGgtatggtggtgttcgtgtgcttgaaaaaatttttctgtgtactttcttctg--ggtttttctatacctttttgct-----ttccttctgattggtttag------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|162170612|gb|FC347108.1|FC347108EST: GAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACG ACGGTGGTCATTAGAGCGCAAGCTGGCAGATGCCGACGTTACAGAAGAGGA
genomic: GAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgc ... acgtcatcagACGGTGGTCATTAGAGCGCAAGCTGGCAGATGCCGACGTTACAGAAGAGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACCCTCAAGTATCACCAGGCAGAAAGTAGCAGCTGCGAAGCAGTATATAGAGAACCACTACAAATCGCAGATGAAGAATTTGCAAGAACGGAAACTACGgtattcatgctgtcttcaattcccttcttcgtggcattccgtcctgttgaatgttccattcgttttctttaagaagatcttttgagtcgtacataaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC