Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ34469 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| | | | || | || || | | | | | | | || | | | |||||||||| ||||| ||||||||||||||||||||| | || |||||||| || || || ||| | || ||||||| ||||| |||||||| |
gtaagttctacaattgttgttaataggttgtaattaatgtagtttaattgatgatcaaatacctcttttttcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 6
------------------gtaagtaatgaaagtta-gttttttctttctctctctctgtcagctcatgtagttggtctggcg----cagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| |||| | ||| | |||| ||||| | || | | | | || |||| ||||||||||| ||| |||||||||||||||||||||| | || |||||||| || || || || | || || || | ||| | ||||| | ||
gtaagtcttattattcctctttgtaacttatattaagaattttgtttctttaaaactaaaatttggttttcttcttctgatattttcagATTCTTGGCAGTAACATGTCAAATAAGATGTGGGAAAGTCTTGTTGAGCATGCGAAGACATGTGTTTTGAGTGGCAAACACTATATATATTACTCAAGCG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
---------gtaagtaatgaaagttagttttttctttctctctc-tctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| || | | || | || | ||| ||| | | || || | || || |||| | ||||| ||||||||||| ||||| |||||||||||||| || || ||||| || || || ||| | || ||||| || | |||||| | ||||
gtaagattatttcctattcagcatttttcttctttttttcttttgtttgagttctaacatatatgttctgtcccagATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g18960.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------gtaagtaatgaaagttagttttttctttctctctct-ctgtcagctcatgtagttggtctggcg--cagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| | || ||| | | | | | | | ||| | | ||| ||| | ||||| ||||| |||||||| ||||||||||||| ||| || |||||||| |||||| || || ||||| || ||| | ||
gtaagaaattaatcatcccttttacaataaaaacttctatttttttagataaacttctctgtccaactttaatgtagcttccatgcatatattctcatcctgaactgcatgtccatttttcagTTACTTGGCAGTGGAATGTCAAACAAGATGTGGGAAGCAACCGTTGAGCATGCACGGGAGTGCGTTCTGGACGACAAGCTTTACTCCTACTGCAGCGGGC
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtaagta--atgaaagttagttt---tttctttctctctctctgtcagctcatgtagttggt---ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
|||||| |||| | | || ||| | | || | | | | | | || | | ||||||| || ||||| |||||||||||||||||||| | || || ||||| || ||||| ||| | || ||||||| ||||| || ||||| |
gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtaagtaatg-aaagttagttttttctttctctctc----tctgtcagctcatgtagttggtctggcg----------------cagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
|||||| | | |||||| ||| || | | | | | | || |||| || | ||||||| || ||||| |||||||||||||||||||| | || |||||||| || || || ||| | || ||||||| ||||| || ||||| |
gtaagttctatgatacctgtttttgcttactatattgtgatttatggtattccctatatggtttgacagcccttgttctttttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctg-tcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
|| | | ||| || ||| | | | | | | | ||| | | | |||||||||| |||||||||||||||||||||||||| || ||||| || || || || || ||||| ||||| || || || || ||| | || |
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgta-gttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| | ||| || | |||| | | || | | | | | | || | | | |||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| ||||| || ||||| || ||| | || |
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| | | | | | |||||| | || | ||| | || || | || | |||||||||| |||||||||||||| || |||||||| | ||| |||||||| || || || || || || ||||| || ||||| || ||| |||| |
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttca-cggat-taactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggt-ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| | || | | | || | | | || | || ||| | | | ||||||||||||||||||||||||||||||||||||| |||||||||||| ||||| || ||||| ||||| ||||| ||| |||| ||| | || |
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
||| | | || | | | | || || ||| | | | | |||||||||||||||||||||||||| | ||||||||| | | |||||| | || || || || | || | || ||| || ||||| ||| |||| |
gtgagtgcacgatttaactatccagtatcttaccaagatgttcaaatattattattcatcatgatgactcttactctgatttt----cagATTCTTGGAAGTGGCATGTCAAACAGGATGTGGGAGACACTTGCAGAGCATTCCAAGACATGTGTATTGAGTGAAATGCTTTACGTCTACTATCCCGAGG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagta---atgaaagttagttttttctttc--------tctctctctgtcagctcatgt--agttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
|||||| || | ||||||| || | | || | | | || | | | | | ||||||||||||| ||||||||||| || |||||||| | | ||| ||||| || || ||||| |||| ||| | ||||| ||| |||| ||||| || |
gtaagtgcttattatgtcaagtttttactcttgaaagagattgttcatggctaatttatctttatccgtttttatctagATTCTTGGAAGCGGCATGTCAAACAAAATGTGGGATGCACTAGTAGAGCACGCAAAGACGTGTGTCCAGAGCAGCAAGCTTTATATCTACTATGCTGAGG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtaatgaaagttagtttt---ttc----tttctctctctctgtcag----ctcatgtagttggt-----ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
||||| | | | || ||| | ||| ||| || ||| | | || || ||| || | ||||||||||||||||||||||||||||||||||||| | ||||||||||| ||||| || || || || || || || ||||| || ||| | || |
gtaagaatgtacattttgttgtcatttcagaatttgaatccgtctattgtaatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaagtaatga--aagttagttttttctttctctctctctgtcagctcatgtagttg---gtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
|| || | | |||| | | ||| ||| || || || || | || | |||| || ||||||||||||||||||||||||||||| | | |||||||| || || ||| | | || |||||| | ||||| |||||| | || |
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------gtaagtaatgaaagttagttttttctttctctctctctgt-cagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| |||| | | | |||| | | | || | | | || ||| | ||||||| |||| ||| |||||||| |||||||||||||| ||||||||||| || |||||||| ||| | || || || ||| |||| ||||| ||||| |
ttcagtatatttggttggggtttcgtaatctgcacacacaatgtatcgtgggttttcatcgttgagttcaagtatttatgacgctgtgtgtcgtgtttagATTCTAGGAAATGGAATGTCAAACAAGATGTGGGAAGGCACAGTGGAGCACGCCAAAACGTGTGTCTTGAGTGGGAAACTGCATGTATATTACGCCGATG
upper sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------gtaagtaatgaaagtt---agttttttctttctctctctctgtcagctcatgtagt----tggtct---ggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
| || | || | ||||| | ||| | |||| | || || ||| |||| | |||||| | |||| || ||||||||||| |||||||| || || ||||||||||| |||||||| || | ||||||||| || |||| ||||| || || |
gtattcttcggtgtaactgcagttatctatactaaatatcttgcagtttttgtacttctatttctggaaccttattaagtgtggtggtttatgaattcagATTTTAGGAAACGGAATGTCAAATAAAATGTGGGAGGGCACCGTGGAGCATGCCAAAACGTGTGTGTTGAGCGGAAAGTTGCATGTGTATTACGCTGATGMapped 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|169082169|gb|FE488016.1|FE488016EST: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAAC ATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
genomic: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
EST:
gi|169058295|gb|FE466036.1|FE466036EST: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAAC ATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
genomic: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
EST:
gi|169051073|gb|FE460206.1|FE460206EST: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACNAAAC ATTCTTGGAAGTGGCATGTCAAATAAAATGTGGGAAGGAACAGTGGAGCAT
genomic: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
EST:
gi|169080154|gb|FE488365.1|FE488365EST: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAAC ATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
genomic: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
EST:
gi|169098535|gb|FE498539.1|FE498539EST: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAAC ATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
genomic: TGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCAT
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),
34 (downstream exon)
Score:
104AAAGGACGGGGCATTCCACAAGAGGCTCAACAAAGCTGGAATATTTTCTGTGGAGGACTTTCTGCGTCTGGTGGTGATGGACCCGCAGAAACTACGAAACgtaagtaatg ... tctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
ttttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaatgaaagttagttttttctttctctctctctgtcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG