Sequence
atgc intronic sequence ATGC exonic sequenceAATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaactagttttccaagtggactttt...
Basic information
species | Physcomitrella patens |
transcript | PP1S38_368V6.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S38_368V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA18G44550.1 (Glycine max), 5'ss of exon 8
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaactagttttccaagtggactttt---
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AATTACTTCTGGTTCATGGGCACTGGAATTATCAGCGTGTTGGTTATTTAGTTCTGTACAACTTCTACCGCAATGCTGTCTTTGTAATGATGTTGTTTTGgtatgtatggttgtccttggatatcacataagttactc---ttgtgtttatataagttggtctctctttccttatttcttttgttatcccctgatgtttcaga
upper sequence: PP1S38_368V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G41040.1 (Glycine max), 5'ss of exon 9
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatg--ccaagttcacatccgctatcaacta-gttttccaagtggactttt----
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AATTACTTCTGGTTCATGGGCACTGGAATTATCAGCGTGTTGGTTATTTAGTTCTGTACAACTTCTACCGCAATGCTGTCTTTGTAATGATGTTATTTTGgtatgtatggttgtccttggatat-----cacacgagttactcttgtgtttacatgagttggtctctctttccttatttctttcgttatccc--tgatctttcagac
upper sequence: PP1S38_368V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv08s0058g01400.t01 (Vitis vinifera), 5'ss of exon 5
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaact--------agttttccaagtggactttt
|||||| || |||||||| |||||||| ||| ||||| | || || ||||||| |||||||| || ||||||||||||||||| ||||||| |||||||| ||||| || || |||| || || | ||| | || | || | | || | ||| || |||||| | ||| ||
GATTGCTTCTGGTGCATGGACACTGGAATTATCAGCGTGTTGGTTATTTGGTTCTTTACAACTTCTACCGCAATGCTGTTTTTGTTTTGATGCTATTCTGgta--tttatgaattttt--atttttttccgttaaccccca-gtt-ctcttaattgtcttttatgtatttgatattggctgaatttgaagttttttatgtgaccta--
upper sequence: PP1S38_368V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ16263 (Selaginella moellendorffii), 5'ss of exon 7
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaactagttttccaagtggactttt
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GGCTTCTCCTCGTCCACGGTCACTGGAACTACCAGCGTCTCGCGTATATGGTGCTCTACAACTTTTACAGGAATGCCGTGTTCGTGATGATGCTCTTCTGgtaagctcact----ctcgtttttcttctcacttttcttcct-ttgtcgttgacatctgcctatag----------------------------------
upper sequence: PP1S38_368V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ17732 (Selaginella moellendorffii), 5'ss of exon 7
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaactagttttccaagtggactttt
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GGCTTCTCCTCGTCCACGGTCACTGGAACTACCAGCGTCTCGCGTATATGGTGCTCTACAACTTTTACAGGAATGCCGTGTTCGTGATGATGCTCTTCTGgtaagctcact----ctcgtttttcttctcactt---------ttcttcctttatc----gttgacatctgcctatag----------------------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|162264922|gb|FC440697.1|FC440697EST: GTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTG GTTCATATTTTATGCAGCTTATTCAGCACAGTCAGCTCTCACTGATTGGAA
genomic: GTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttat ... gcttaaccagGTTCATATTTTATGCAGCTTATTCAGCACAGTCAGCTCTCACTGATTGGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATTGCTCCTCGTGCATGGTCACTGGAACTATGAGCGTTTGGGCTACATGGTTCTCTACAACTTTTATCGCAATGCTGTTTTTGTAATGATGCTTTTCTGgtaaatttattgcttcttgaatttgcttttatttggttgaatgttgtttttgaatgccaagttcacatccgctatcaactagttttccaagtggactttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT