Sequence
atgc intronic sequence ATGC exonic sequencegtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ13132 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os09g19800.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------gtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
| | | ||||| || | | | | | | | ||| | | || |||| || || |||| | || || | |||||||| |||||||| |||||||| || |||||||||||||| || | |||||||| || |||||||| |
tttacattacagtttttaagaatgatttcatattgagatattttccttgggtgatcaagtagtttat-atgtaa-atctctgtccacatctgttc-tgtttagGTAGCAATTACTGTCGCGCATGAATTGGCTCATCAATGGTTCGGCAATCTTGTAACCATGGAATGGTGGACTCACTTGTGGCTAAACGAGGGTTTTGCTA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os08g30810.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------------------------------------------------------gtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
| || | | | | | | | || ||||||| | ||| | || || | |||||||| ||||| || |||||||| || ||||| |||||||| || | ||||||||||| ||||||||
gttatgcctatatttatctttatcaatttcatttgtttcatttactattggagagttagtctcgcacttgaatcctcatgtgtagttttggccaggtaaactgctatttttaaaaaagaaagaaagaaagaaaaattaacatctgttctctttagGTTGCAATCACTGTTGCACATGAATTGGCTCATCAATGGTTTGGCAATCTTGTAACCATGGAGTGGTGGACTCACTTGTGGCTAAATGAGGGTTTTGCTT
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os09g19790.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------------------gtattacatgctagttcattgttt---ggtgtt----tttaccgagtgt-------tgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
||||| | ||| || || | || || ||||| ||| | |||| ||||||| || || | || || || |||||||| ||||| || |||||||| || |||||||||||||| || | |||||||| || |||||||| |
gtatatatcataactcagattctttttagttacatatttcatcatttatggttcactttgtaaatagtgatgcattattatttattagacattttctttgggacgtccaaattccttcagtgtaagcaactgttc-tttttagGTTGCAATTACCGTGGCACATGAACTGGCTCATCAATGGTTTGGTAATCTTGTAACCATGGAATGGTGGACTCACTTGTGGCTAAACGAGGGTTTTGCTA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g12650.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------gtattacatgctagttcattgtttggtgttt---ttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
|| | || | | ||| | | | | | | | || | | |||||||||| ||||| || | || || | ||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||| || || |||||||| |
atttaataatttctgatattcatatctgttttggttgtcatgtttaattgataccatccttctgtaagatacgtagctaatctcttattccac-tgttcagGTTGCAGTTGTGGTAGCCCATGAATTAGCTCACCAGTGGTTTGGAAATCTTGTGACGATGGAGTGGTGGACACACCTATGGCTTAACGAGGGTTTTGCGA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G027875_T01 (Zea mays), 3'ss of exon 7
-------------------------------------gtatta-catgctagtt-cattgtttggtgtttttaccgagtgttgtgcatttt------cagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
|| | || | | | || || |||||| |||| |||| |||||||| |||||||| |||| || | |||||||| ||||| ||||||||||| ||||||||||||||||| ||||| ||||| ||||| || ||||| |
ggattgatcagatttgcagtagctgttttatttccatgtgctgtcacaccaactatatataatgatgttttgctattcctttgtatatttctttatccagGTTGCAGTTGTTGTAGCTCATGAATTAGCTCATCAATGGTTTGGAAATCTTGTCACAATGGAATGGTGGACACATCTGTGGCTTAATGAGGGCTTTGCGA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G090542_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------gtattaca-tgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
| |||| | || | | | | | ||| || || | | | | |||| || | ||| | || ||| | || || || ||||| || |||||||| || |||||||||||||| || | ||||||||||| ||||||||
gtttttgataatatttaaatcaaatccatttatttcataagctaataattgatgactgttgccaagattgctttgctacaattataaccaagtatatctcctcttttccccttgatatctttacttagGTAGCAATAACTGTTGCACATGAGTTGGCGCACCAATGGTTTGGCAATCTTGTGACTATGGAATGGTGGACTCACTTGTGGCTAAATGAGGGTTTTGCTT
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA04G05620.2 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------gtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcatt----ttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
| | || | | | | || | | | | | || || ||||||| ||| || |||| || || || || |||||||| || || |||||||||||||| |||||||| ||| | ||||| ||||| || |||||||
gtactctgcttatccataaagttgatttggtatcagctacttgagtttccattctaaattttaagaactaataattttgttactaactgaaggacaaaatatatttctttggttactgtttagGTTGCAACTGTAGTAGCTCATGAACTAGCACACCAGTGGTTTGGCAACCTTGTTACAATGGAGTGGTGGACACATTTGTGGCTGAATGAGGGGTTTGCAA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT4G33090.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------gtattacatgctagttcattgtttggtgtttttaccgagt--gttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
||| | | | |||| | | | | ||| | | | ||||||| ||| || |||| || || || || |||||||| || ||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| |
gtactgtaaacatgtccatttattctctagaggaaattgtcttgtgctctcttgtgcaattatctaaagcagttaaatttctgctgctagGTTGCCACTGTAGTTGCTCATGAACTGGCCCACCAGTGGTTTGGCAATCTTGTTACTATGGAGTGGTGGACTCATCTATGGCTGAATGAGGGTTTTGCTA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv09s0002g01900.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gtattacatgctag---ttcattgtt--tggtgtttttaccgagtgtt-gtgcatt-ttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
| | ||| || |||| || ||| ||| | |||| ||| | ||| || | ||||||| | ||||| | || ||||||||||| || || || || ||||||||||||||||| ||| | ||||| ||||| || |||||||
gtactctcatactgcaaaacaataaaacaaatggtaaaaaggcattattgccaacagtttcaccaaatgtttgtgttctacccagCTTACAATTGTTGTGTCACACGAAGTGGCCCATCAGTGGTTTGGGAACCTCGTAACAATGGAATGGTGGACTCATTTGTGGCTTAATGAGGGGTTTGCAA
upper sequence: EFJ13132 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S292_64V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------gtattac--atgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
|| || || | || | || || || ||| ||| | |||||| ||||| || || |||||||||| || ||||||||||| ||||||||||| || ||||| |||||||| ||||||||||| || ||||||||||| |
gaagtgcatgagttttataaatgttgcattttaaaatatcttagtcctatgaatttcatttaagaacatgagattgtttgcgatgtttgctggtaatcagGTCGCTGTGGTCGTGGCTCACGAGCTGGCACATCAGTGGTTTGGAAATCTTGTCACCATGGAGTGGTGGACCCATCTTTGGCTTAACGAAGGTTTTGCCAMapped 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|169022905|gb|FE431518.1|FE431518EST: TGCTCTTCTCTTTGATGAGAAGCATTCGGCTGCCGCGAACAAGCAACGA GTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTT
genomic: TGCTCTTCTCTTTGATGAGAAGCATTCGGCTGCCGCGAACAAGCAACGAgtattacatg ... gcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTT
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:
29 (upstream exon),
34 (downstream exon)
Score:
7CTTCGCAGCTGGAGCAATGGAAAACTATGGCCTTGTTACTTACCGTGAGACTGCTCTTCTCTTTGATGAGAAGCATTCGGCTGCCGCGAACAAGCAACGAgtattacatg ... gcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
cattttc CT-rich tract
tgttttta TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattacatgctagttcattgtttggtgtttttaccgagtgttgtgcattttcagGTTGCTGTTGTTGTCACTCACGAGCTTGCTCATCAGTGGTTCGGAAATCTTGTTACAATGGAATGGTGGACGCATCTTTGGCTAAATGAAGGTTTTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA