Sequence
atgc intronic sequence ATGC exonic sequenceTACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaactggaatttggtttgcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14101 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 10
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaa-------gtgcaatttc----gtgttctatgtttttaactggaatttggt--ttgcag--------------------------------------
||||||||||||||| || ||||| || || || || |||||||||||||||||||| || ||||| |||||||| || ||||| |||||||| || || |||| || |||| || | || ||| |||| || |||| |
TACAATGGGGATGCTTAGCACAGCAGCATATGTTCTCACCATGGACATGTTTGGTCCAATAGCTGACAATGCTGGTGGTATTGTGGAGATGAGTCAGCAGgtaatacactcgtattttttcccatgtatatagcagttcaaaccaatattttgtctttgctgtaggtttttatttaccgtttctgttaatatgctttact
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 10
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaactggaatttggtttgcag----------------------------------------------------
|||||||||||||| || ||||| | ||| || || |||||||||||||||||||| || ||||| |||||||| || ||||||||||||||||| || ||| || || | || || | | | ||| | | | || ||
GACAATGGGGATGCTTAGCACAGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAATGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatacacatgtttcttttgta-gctcaaacctgtgctgtagcctgtaggttgtagcaacaatctgtattatttagtgcttttgccattacaaaatttcaa
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaac-tggaatttggtttgcag---------------------------------------------------
|||||||||||||| || || || | ||| || || |||||||||||||||||||| || ||||| || ||||| || ||||||||||||||||| || ||| | ||| | | || ||| | ||| | | | | | ||
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatg-gcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA08G24120.4 (Glycine max), 5'ss of exon 9
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgta---------agtgcaatttcgtgttctatgtttttaactggaatttggtttgcag---------------------------
|||||||| ||||| ||||| ||||| || | || |||||||| |||||||| || || |||||||||||||| |||||||| |||||||| || || ||| || ||||| || ||| || ||| ||| |||
AACAATGGGAATGCTTAGTACTGCTGCCTATATTCTTACCATGGATATGTTTGGCCCAATAGCTGATAATGCTGGAGGAATTGTAGAGATGAGTCAGCAGgtagttcttgctagaataatttggtccatagagttcttt-ctgtgattcctcatgccatgtgtactgactattaacctttttcag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 10
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgta---------agtgcaatttcgtgttctatgtttttaactggaatttggtttgcag----------------------------
|||||||| ||||| || || ||||| || | || |||||||| |||||||| || || |||||||||||||| |||||||| |||||||| || || ||| || ||||| || |||| || ||| ||| ||||
AACAATGGGAATGCTTAGCACTGCTGCCTATATTCTTACCATGGATATGTTTGGCCCAATAGCTGATAATGCTGGAGGAATTGTAGAGATGAGTCAGCAGgtagttcttgctagaataatttggtccatagtgttattt-ctgagattcctcttgctatgtatactgactattaacctgttttcag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 11
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaat------ttcgtgtt----ctatgtttttaactggaattt---ggtttgcag---------------------
||||||||| ||| |||| || || || || || || || |||||||||||||||||||| ||||||||||| || || ||||||||||||||||| || ||| | | || |||| || ||||||| | | |||||| | || |
TACAATGGGAATGTTGAGCACTGCAGCTTATGTTCTTACAATGGACATGTTTGGTCCCATAGCTGATAATGCAGGTGGGATTGTTGAGATGAGCCAGCAGgtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttctataaaacttatcgtgtcttgcag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 10
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaag-tgcaat----ttcgtgttctatgtttttaactggaatttggtttgcag--------------------------
||||||||| ||||| || || || || || || || || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||||||||| || ||||| || | || | | | | | ||| | || | || |
TACAATGGGAATGCTAAGCACTGCAGCTTATGTCCTTACTATGGACATGTTTGGCCCCATAGCTGACAACGCTGGTGGGATTGTCGAGATGAGCCAGCAGgtaagatgtcacatgattggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 10
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaa-----gtgcaatttcgtgttcta-tgtttttaactgga---atttggtttgcag-------------------------------------
|||||||| |||||||| || ||||| || || || || ||||| ||||||||||| || |||||||||||||| ||||| || |||||||| || || ||| | ||| | | || | | | || ||| | | | | ||
AACAATGGGAATGCTGAGCACTGCTGCCTATGTTCTAACTATGGATATGTTTGGTCCAATAGCTGATAATGCTGGTGGAATAGTAGAGATGAGTCAGCAGgtagccattctacaactgaatttttcaataatgttggctgaatcaaaaggaactttagtgctttgtttttaacttgatacaaaatgctcttacag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 5'ss of exon 11
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaac-tggaatttggtttgcag----------------------------------------------------------------
|| ||||| ||||| ||||| |||| |||||| |||| |||||||||||||| |||||||| || |||||||| || |||||||| ||||| ||||| || || || ||| || | | | | | || | || |||||| | |
AACTATGGGCATGCTCAGTACCGCTGGTTACGTGTTGACAATGGACATGTTTGGACCCATTGCAGACAATGCTGGAGGTATTGTTGAAATGAGTCAACAGgtgagggcg--ttcatgatttttttctatatcatgttctttggtgtaatgaactcgttgaacttttgtatttgggtgtcggcttcgttgattcctgttaacgtaatggttgcag
upper sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgtt-ctatgtttttaactggaatttggtt-tgcag-----------------------------------------------------
|| ||||| ||||| ||||| || | || ||| |||| |||||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||| ||| | | | | | | |||| | | || |||
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagMapped 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|169099967|gb|FE503455.1|FE503455EST: TTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAA CCGGAGAGCGTGAGAGATATTACTGATGTTCTTGACGCAGTCGGCAACACT
genomic: TTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaa ... tggtttgcagCCGGAGAGCGTGAGAGATATTACTGATGTTCTTGACGCAGTCGGCAACACT
EST:
gi|169078439|gb|FE488314.1|FE488314EST: TTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAA CCGGAGAGCGTGAGAGATATTACTGATGTTCTTGACGCAGTCGGCAACACT
genomic: TTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaa ... tggtttgcagCCGGAGAGCGTGAGAGATATTACTGATGTTCTTGACGCAGTCGGCAACACT
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:
30 (upstream exon),
32 (downstream exon)
Score:
8TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaa ... tggtttgcagCCGGAGAGCGTGAGAGATATTACTGATGTTCTTGACGCAGTCGGCAACACTACCAAGGCAACAACCAAGGGATTTGCTATAGGCTCCGCTGCGTTAGCAT
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaactggaatttggtttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG