Sequence
atgc intronic sequence ATGC exonic sequenceGATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctgattccag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ16760 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctcttta---gatgggaattctaaccgtgaatgtctgattccag-----------------------------------------
||||| | |||||||| || || |||||||||||||| || || ||||| ||||| || |||||||| || || ||||| ||||||||||||||||| || || | | ||||| || | || | || | ||| ||| |
AATGAGTGCGTCCAGGTTCATCAAGTGTGTCACTGTGGGTGACGGTGCCGTTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgctacttttctcactatcgcaaacaaagcttcacattttctgttctcttcaggttctagcttactgggttttcagataatcacaaatagttggg
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctgattccag----------------------------------------------
||||| | |||||||| || || |||||||||||||| || || ||||| ||||| || |||||||| || || ||||| ||||||||||||||||| || || | | | || | | | | | ||| |||| ||| |
AATGAGTGCGTCCAGGTTCATCAAGTGTGTCACTGTGGGTGACGGTGCCGTTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcag--tgctaccactaacaaaccttcacatttttctgtgctcttctgcttctaccttactgggttttcagataataatgacaaaatatggcttgttatca
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 2
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttct-tctctttagatgggaattctaacc-----gtgaatgtctgattccag--------------------------------------
||||||| |||| ||||| || || || |||||||| || ||||| || || |||||||| ||| |||| ||||| ||||| ||||||||||| || || || || | |||||| |||| | | | |||| | || | | || |||||
GATGAGCGCTTCTAGGTTCATCAAGTGCGTCACTGTTGGGGATGGTGCTGTGGGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACCgttagttcttttctctctcctaaaaactaaattttgggttctgggtaattctccaattccgcatattttgaataaattcagctacgtttgcatttaatct
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA16G23340.1 (Glycine max), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctgattccag--------------------------------------------
|||||| |||| ||||| || || ||||||||||| || ||||| ||||| |||||||| || ||||||| || ||||| |||||||| || || ||||| || | |||| ||| || | | | | | | || | ||
-ATGAGCGCTTCTAGGTTCATCAAGTGTGTCACTGTCGGGGATGGAGCCGTGGGCAAAACTTGTTTGCTAATCTCCTACACCAGCAACACCTTCCCCACTgttagttcttttattcctctttttttgtttctttgtgtattagtgacaatttttttatttcccttttttggaatgcattttagagctttggatttaaaaa
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA01G36880.4 (Glycine max), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctcttt----agatgggaattctaacc-----gtgaatgtctgattccag-----------------------------------
||||||| |||| ||||| || || || |||||||| || ||||| || || |||||||| || |||| ||||| ||||| |||||||||||||| || || || || ||||| | | | |||| | || | ||| |||||
GATGAGCGCTTCTAGGTTCATCAAGTGCGTCACTGTTGGGGATGGTGCTGTGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtacttcctttctcccttctaaaaacataattttgggttctgggtaattgttctattccgcaatttatgaagaaattcagctgcatttgcatttca
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTAC--Tgtgagattttttcttctctttagatgggaattctaa--ccgtgaatgtctgattccag-------------------------------------------------------------------------------------------------------------------------------------
|||||| |||| ||||| || || |||||||| || || || || || || || ||||| || |||| ||||||||||| ||||||||||||||||| | | | || ||| | || || | | | |||||| | | ||
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt--ttcttctctttagatgggaattcta--accgtga--atgtctgattccag----------------------------
|||||| |||| ||||| | || || || || || || ||||| || ||||| ||||| || || | ||||||||||||||||||||||| ||||| || | | || |||| | | | || | ||| | | | || ||
AATGAGCGCTTCGAGGTTCGTAAAGTGCGTGACGGTTGGTGATGGAGCTGTCGGAAAAACTTGTTTGTTGATTTCTTACACAAGCAACACTTTCCCTACGgttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgtttcttgtttcttttgtggatatacag
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctga---ttccag-----------------------------------------
||||||| | || |||||||| || || || || || || ||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||| || || | || | || || || | || | | || || ||
GATGAGCGCCTCTAGGTTTATAAAGTGCGTTACGGTCGGTGATGGTGCTGTCGGCAAAACCTGCATGCTGATTTCCTACACCAGCAACACTTTCCCTACGgttagttccccattttctgattctaggtttttgtatctttggttcttggaaagatcgagggaaagcaagaggaaccaaaagaaaatgctctaaaagaaaa
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 5'ss of exon 2
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattt-tttcttctctttagatgggaattctaaccgtgaatgtctgattccag-------------------------------------------
||||| |||| ||||| ||||| || |||||||| || || || ||||||||||| || |||||||| || || ||||| ||||||||||| || || || || | | ||| | | ||| || | | ||| || || |
AATGAGTGCTTCAAGGTTCATTAAGTGCGTCACTGTCGGTGACGGCGCCGTCGGCAAGACTTGCATGCTTATCTCCTACACCAGCAACACTTTCCCCACGgtcagctctgtttttggtttttcttcctttttttttttttttgctgtttggttttcgagaaaatgaagtaggagaaaggggaattgggctttttgagtgt
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctgattccag--------------------------------------------
||||||||||| ||||||| || || || ||||| |||||||| || ||||| || || |||||||| ||||| ||||| |||||||| ||||||||||| || | | || | || | | ||| | ||||
-ATGAGCACTTCACGGTTTATCAAGTGCGTGACTGTTGGAGATGGAGCTGTCGGGAAGACGTGCATGCTTATTTCATACACCAGCAACACATTTCCTACTgtaagcaacgactgcttgtggagtggtctatcatctggataggtgttggtttcctaagtttcattcggttgctgaatccctcaacaagaattacggatct
upper sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgt--ctg-attccag-----------------------------------------
|||||||| || ||||||| || || || ||||| |||||||| || ||||| || || |||||||| |||||||| || ||||| || ||||||||||| || | | | ||| | | | | || | | || | ||| | || |
-ATGAGCACATCTCGGTTTATCAAGTGCGTTACTGTAGGAGATGGAGCAGTCGGAAAGACGTGCATGCTTATTTCTTATACCAGCAATACATTTCCTACTgtaagctgcgaccgtttctggacaggcgctttttcatgacagatttcactgcactctatgtttatttggcattattatcagtttccgtcccattacgtctMapped 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|169038008|gb|FE445813.1|FE445813EST: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACT GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
genomic: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
EST:
gi|169075481|gb|FE482491.1|FE482491EST: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACT GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
genomic: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
EST:
gi|169075482|gb|FE482492.1|FE482492EST: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACT GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
genomic: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
EST:
gi|169110406|gb|FE512165.1|FE512165EST: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACT GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
genomic: TCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
EST:
gi|169110405|gb|FE512164.1|FE512164EST: ACACAAGCAACACTTTTCCTACT GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
genomic: ACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGAT
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:
35 (upstream exon),
35 (downstream exon)
Score:
20GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagatttt ... ctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTACTgtgagattttttcttctctttagatgggaattctaaccgtgaatgtctgattccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA