Sequence
atgc intronic sequence ATGC exonic sequenceTGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ21576 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag------------------------------------------------
||||||| || |||||||| || ||||| || || || || || ||||||||||| || || |||||||| |||||| | ||||| || || ||||||||||| || || | | | || || | | | | | |
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatgga---cgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagtt------ctcgcgaaacctttcttagggtttttgaatgtcggttctttc-ttacag-----------------------------
||||| | |||||||| || || ||| |||||||| || ||||| || || || ||||||||||||||||| ||| | ||||||||||| || || |||| || | || || | | | ||| ||| | | | || | | ||| |
TGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAACAATATAATGCTTTGGAATGCTGTAATTTTTGGgtaaggtgttagacttaagagatatgttttattcctttcggttttattttgatccattatacttagttgtcaattatgtcttgttttgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 1
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctt----tcttagggtttttgaatgtcggttctttcttacag--------------------------------------------------------------------------
||||||| || ||||||||||| ||||| || || || || |||||||||||||| || | ||||||||||||||| | ||||| || || || ||||||| | ||| | | | ||||| | | || ||| |
TGATGCGGGACTTCAAGCGCCTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGTACGACAACAATATCATGCTCTGGAACGCCGTCATATTCGGgtatcagcccgcctatttctgtgatgttaggttagctagcctaaggatctagtgaggcgtgaggccgcgatacttttggtgggttttaatgctgactgtgctttttctcttggtgtttgttgcgattctgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag-------------------------------------------------------------------------------------------------
| ||| ||||||||||| | || || || || ||||| ||||| ||||| ||||| || ||||| ||||| |||||| ||||||||||||| || || ||||||| | |||| || || | | || | | | | |
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaa--ttggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.3 (Glycine max), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag-----------------------------------------------
| ||| ||||||||||| | || || || || ||||| ||||| ||||| ||||| || ||||| ||||| |||||| ||||||||||||| || || ||||||| | |||| || || | | || | | | | |
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaa--ttggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgta
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 3
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcg---aaacctt----tcttagggtttttgaatgtcggttctttcttacag-------------------------------------------------------------------
||||| | ||||| || | | || || |||||||| || |||||||| || ||||| || ||||| ||||| ||| | ||||||||||| ||||| ||||| || | ||| | | | || | || || | ||| ||| | ||||
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G40860.1 (Glycine max), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagt----tctcgcgaaacct---ttcttagggtttttgaatgtcggttctttcttacag-------------------------------------------------------------------
||||| | ||||| || | | || || |||||||| || |||||||| || ||||| || ||||| ||||| ||| | ||||||||||| ||||| ||||| || | | || ||| || || | || || | ||| ||| | ||||
TGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGgtgtgtaggagtttacaaatcctgtattttttgttttcttaagtgtgtgtttctctttactttgtggttgtggatggtttaatgtatagtaacaatctaattgtgccttttcttggtgcttttttccag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G16160.3 (Glycine max), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcg---aaacctt----tcttagggtttttgaatgtcggttctttcttacag--------------------------------------------------------------------
|||| | ||||| || | | || || |||||||| || |||||||| || ||||| || ||||| ||||| ||| | ||||||||||| ||||| ||||| || | ||| | | | || | || || | ||| ||| | ||||
-GATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACAATAATATTATGCTTTGGAATGCTGTTATCTTTGGGtgtgtaggagtatataaatcatgaaatttttgttttcttaagtgtgtgtttctctttactttgtggttttggatgatttaaggtatgataacaatctaattgtgcttttcttggttctttttttccaga
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag----------------------------------------------------------------------------------------
||||| |||| |||||| | || || || || || || ||||| |||||||| || || ||||| ||||| || ||| ||||||||||||| || || ||||||||| ||| |||| | ||||| | || | ||| ||
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttgaattcaaattcgatatagg----tccaatgttg-ttttaatttatagtcaattggtcactattttttaatttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagtt--ctcgcgaaacctttcttagggtttttgaatg-tcggttctttcttacag---------------------------------
||||| | ||||||||| | | ||||| || || || ||||| || || || |||||||| ||||||||||||||||||||||||||||| || ||||||| | | || | ||| | | || | |||| | || |
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 5'ss of exon 1
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagt-tctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag----------------------------------------------------------------------
||||| | ||||||||| | || ||||| ||||| || || |||||||| || ||||| ||||||||||| |||||| | ||||||||||| || || |||| | | || ||||||| ||||||| || || | |||||
TGATGAGGGATTTCAAGAGGCTCCAGCAAGATCCACCTGCTGGCATCAGTGGGGCTCCTCAGGACAACAACATCATGCTATGGAATGCTGTCATTTTTGGgtatttctttctttctctctttctttctttttttgattggtt-ttttgccttaccattttgtttatcaacttgttttgataattctaattctgggtttttggtgttttttcttgtttgatttgtag
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag-----------------------------------------------
||||||| || ||||||||| | || |||||||||||||| ||||||||||||||||| |||||||||||||||||| |||||||||||||||| ||||||| | | | || | || | |||||| || | |
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaa--cgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt
upper sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtg-----agttctcgcgaaacctttcttagggtttttga--atgtcggttctttcttacag--------------------------------------
||||||| || ||||||||||| ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||||||||||| || ||||||| | | ||| | | | | | | | | ||||||| |
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggtttMapped 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|169060608|gb|FE467346.1|FE467346EST: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGG GCCTGACGACACGCCATGGGATGGAG
genomic: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctc ... tttcttacagGCCTGACGACACGCCATGGGATGGAG
EST:
gi|169054452|gb|FE460274.1|FE460274EST: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGG GCCTGACGACACGCCATGGGATGGAG
genomic: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctc ... tttcttacagGCCTGACGACACGCCATGGGATGGAG
EST:
gi|169060609|gb|FE467347.1|FE467347EST: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGG GCCTGACGACACGCCATGGGATGGAG
genomic: GGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctc ... tttcttacagGCCTGACGACACGCCATGGGATGGAG
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:
32 (upstream exon),
33 (downstream exon)
Score:
18TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctc ... tttcttacagGCCTGACGACACGCCATGGGATGGAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATGCGAGATTTCAAGCGCCTACAGCATGATCCTCCGGCAGGCATCAGCGGCGCTCCACAGGACAACAATATCATGTTGTGGAATGCTGTGATCTTCGGgtgagttctcgcgaaacctttcttagggtttttgaatgtcggttctttcttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG