Sequence
atgc intronic sequence ATGC exonic sequenceGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ27201 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggt-----gttcgtcagctctcctgttttga----ggatt---ttctattgtc--tagaggatt-atgtgtgg-----gatctttgtggcag----------
| || ||||| || ||||||||| | ||| | ||||| || ||||||||||| ||||||||| |||||||| || || |||||||||||||| |||||| | || || | || | | | ||||| ||||| || || | | ||||| |||| || |||||| |
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTGAAATCACTGACAAGCTTCGGCAAGAAATCAATAAGgtttttcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtag
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttc-----gtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag----------------------------
| || ||||| || ||||||||| | ||| | |||||||||||||||||||| || ||||| |||||||| || ||||| ||||||||||| ||||| | | | | |||| || ||| ||| | | | | || | |||| |||| | |
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTGAAATCACTGAGAAGCTACGACAAGAAATCAATAAGgtattcaaatttcccatgtagcagcactgctgcttttaaaagtggaccacatttaataaac-atgt-caggattggcatatgatctttaacatctatactgtatgttgctag
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G018697_T03 (Zea mays), 5'ss of exon 7
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctag--aggattat-gtgtgggatctttgtggcag-----------------------
| || |||||||| ||||||||| | ||| | ||||| ||||||||||| || ||||||||| ||||| || |||||||| |||||||| || |||||| | | || | | | | | ||| | || | | || | |||| | | | || ||| | |
TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacag
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgtta-gccggtgttcgtcagctctcctgttttg-------aggattttctattgtctagaggattatgtgtgggatctttgtggcag----------------------
| || |||||||| ||||||||| | ||| | ||||| |||||||||||||| |||||||| ||||| || || ||||| ||||||||||| |||||| | | || |||||| | | |||| ||| | | | || | || |||| | ||||| |
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgta-agaatcttcacctgattttaaattttacatggtgaaag
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgt----tagccggtgttcgt-cagctctcctgttttgaggattttctattgtctagaggattatgtgtg--------ggatctttgtggcag--------
|| |||||||| |||||||||||||| || | ||||| |||||||||||||| | || || ||||||||||| || | |||||||||| |||||||| | | || | || | | |||| | | || | || |||| | || | ||| | ||
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAGAGATCACTGACAAGTTGAGGCAAGAAATTAACAAGgtattttcataacttttgatacaagtttgtagtttcatctttaattagttatggggaaaattaagggtctaaaaaatgagcttttttcttagcaatttct
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtggga-------tctttgtggcag-----------------
|| |||||||| |||||||||||||| || ||||||| |||||||||||||| | || || || |||||||| || | ||||||| || |||||||| | | | | |||| | || | || | | |||| | || | | ||||| ||
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGACAAGTTGAGGCAAGAGATTAACAAGgtattttaataacttttga---tacaagtttgtagtttcttatttatgggaaaaattaagggtcgaaaagtgagcttttgtcttagcaatttgttcaattgct
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagc--cggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag-----
|| ||||||||||| || ||||| ||||| ||||||| || |||||||| ||| |||||||||||||||||||| || ||||||||||| |||||||| | || | | | | | |||| || || || || ||| | | | | | | | || ||
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgattt-ttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag---------------------
|| |||||||||||||||||||| | ||| | ||||| |||||||||||||| | || || || ||||||||||| |||| || ||||| |||||||| | | | | | | | ||||| || | | || || | || | | |||
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt
upper sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 7
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttt-tgaggattttctattgtctagaggattatgt-gtgggatctttgtggcag-------------------------------------------------------------------
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TCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTGAAATTACTGATAAATTACGACAAGAGATTAACAAGgtaattt--ttcttgac-gctgtgctgtgagtatggacaagaaacctcgtacaaagtcgtgttgtaacattatattattaatcaagaggtaatgctgagtcagaagggcaacgagtttgagatggtttctcgttcatttgtggtgcagMapped 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|169060614|gb|FE467352.1|FE467352EST: AGCCGAAAAAGACTGAGATCACTGATAAGCTGCGGCAGGAAATCAACAAG GTGGTTAATAGGTATATTGATCAAGGAGTGGCGGAGCTTGTACCTGGTGTC
genomic: AGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggt ... tttgtggcagGTGGTTAATAGGTATATTGATCAAGGAGTGGCGGAGCTTGTACCTGGTGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA