Sequence
atgc intronic sequence ATGC exonic sequenceATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31527 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA02G46780.1 (Glycine max), 5'ss of exon 11
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatg-gtctttttatgac-gatag--------------------------------------
||||||||||| ||||||||||||||||| |||||||| ||||| ||||| ||||| || || ||||| |||| |||| | | | || | | ||| ||||| | ||| || || || ||
ATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAGgtaaatgcttgtgcttaatctttactttgttt----cttttaaatttatttttaaataactgaaagtgaagcatatattgaattcatccatctttactctgttt
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA14G01920.1 (Glycine max), 5'ss of exon 11
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatg-gtctttttatgac-gatag--------------------------------------
|||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| || || ||||| |||| |||| | | | || | | ||| ||||| | ||| || || || ||
ATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAGgtaaatgcttgtgcttaatctttactttgttt----cttttaaatatatttttaaataactgaaagtgaagcatatattgaattcctccatctttactctgttt
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 5'ss of exon 11
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttt-tgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag-----------------------------------------------------------------------------------
|| ||||| || |||||||| || || ||||||||||| ||||||||||| |||||||||||||| || ||| | | | | || | || || | | ||| || |||
ATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAAgtaagtgccctagtttcaactctttaagaaaatcgtcattctagacctacatttctagagaatattaacctatatcttacataacttatttgcccattagtaaggctctattccattgcttatggcctccatgattttggctcaatag
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 5'ss of exon 11
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgt---tttgctttgttctta--ttgctgatgttttctgaagctta--taaatggtct---ttttatgacgatag--------------------------------------------------------------
|| ||||| || |||||||| || || ||||||||||| ||||| ||||| ||||||||||| ||||| | | | | | ||| || || | | | | | ||| || || | || | |
ATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAGgtaagctcatcctagtttcagcttgttgccattcttcaaggttgggttgaatagtaggagattcagaacaaaacgggttatatctgagagcagaggagattcaaatttctcacttccattgttttgggctcaatag
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 5'ss of exon 13
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag-------------------------------------------------------------------------------------------------------------------------
|||| ||||||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||||||| || || | | | || | |||| || ||||| |||||| | | |
GTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAGgttggttatttccctgaattcctat----tttgaaaactagaaatg-cctttttgtctcaaccctcgctactggttcatgagctttcagttcaagggactttgcagggtagttatgctaaaacttatatttgtgtatgtacatcaccatccttaaacttctctgctcatggaaatttgtttccag
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S58_81V6.1 (Physcomitrella patens), 5'ss of exon 14
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag----------------------------------------------------------------------------------------------------------------------------
|||| ||| ||||||| |||||||| || |||||||| ||||||||||| ||||| ||||| |||||| || ||||| | | |||| | ||| ||| ||| | |
GTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAGgttggtgatttcgtttattcaatgtttattctttgctgtgggaatttcttttctatttgtttggattctcatagagcatttcatgagctgtcaggttaagagagcactggagagttttcatacagaaacttgtatatttttttatattgcgttacatcaccaggcggtgcttggcattttgaatgcag
upper sequence: EFJ31527 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 5'ss of exon 14
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag-------------------------------------------------------------------------------------------------------------------------
||||||| |||||||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||| | ||||| | | | || | || | | || ||||| | ||||
GTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAGgttggtcattgtttacaa----ggtcttgtttgggaatgaacaaca-tctttctgaatcgatccttgcaaccagctcatgagctgccacgttaagagatcatgcacatttactatgctgaggtgcatacttgtacacctatatcatcaggctttaattggggggctcttggacttgtgaatgcagMapped 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|169030235|gb|FE439258.1|FE439258EST: TTGAGTAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG GAAGAGATACGACGAAAGACCGGCTATGTAGTCCAAAGAGCTGAAGGTGTA
genomic: TTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgcttt ... atgacgatagGAAGAGATACGACGAAAGACCGGCTATGTAGTCCAAAGAGCTGAAGGTGTA
EST:
gi|169043934|gb|FE453847.1|FE453847EST: ATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG GAAGAGATACGACGAAAGACCGGCTATGTAGTCCAAAGAGCTGAAGGTGTA
genomic: ATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgcttt ... atgacgatagGAAGAGATACGACGAAAGACCGGCTATGTAGTCCAAAGAGCTGAAGGTGTA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
33 (upstream exon),
27 (downstream exon)
Score:
10ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgcttt ... atgacgatagGAAGAGATACGACGAAAGACCGGCTATGTAGTCCAAAGAGCTGAAGGTGTATTTGATGTTGATGCTAATACATCAATCGAGGATCTGTCCGAGGCTTTGC
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAGgttttgctttgttcttattgctgatgttttctgaagcttataaatggtctttttatgacgatag
- - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - GGAGAA