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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctag

Basic information

species Selaginella moellendorffii
transcript EFJ06060
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g60870.1 (Oryza sativa), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaat-tccttctttcta-tggtggtggtgttcttcccggacgg-atggaactctag------
|||||| || |||||| | ||||| ||||||| |||||||||||||||||||||||||| ||||| || || ||||| ||||| || |||||| ||||||| | || | | ||| || | | || | | | | ||| || | ||| ||| | | | | | | || | || |
CGTCGGCAAGTCCAACATCCTCTCGCGATTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATTGGCGTCGAGTTCGCCACCCGCACGCTCCAGgtcccccttccctcgcgcgatccatcctcttctctcgcgactatggttcagaatagtagtgttggggatttcgcatgtcaccattgcgttcgatgcattt

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g01480.1 (Oryza sativa), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaa--caaagaattctctctttccctctt--------ttctcatctcaaattccttctttctatggtggtg-gtg--ttcttcccggacggatggaactctag
|||||| || |||||| | |||||| | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |||| ||| | | | |||| |||| || | | || | | | | || || | | || | || | ||| | | || || |
CGTCGGCAAGTCCAACCTCCTCTCCCGTTTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTCCATgtatgtccatctttcatctccttccttcctgcttactgtacttaccactagctctagctaccctagctgcttcgtaattcctttctcaatcaattcaatt----

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g62950.1 (Oryza sativa), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaac-----aaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacg----gatggaactctag
|||||| || |||||| | |||||| | ||||| ||||||||||||| |||||||||||| ||||| ||||| ||||| ||||| || ||||| | |||||| | | | | | | ||| | | | || | | | ||| || | || || || || |||| | |
CGTCGGCAAGTCCAACATCCTCTCCCGCTTCACCCGCAACGAGTTCTTCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTGCAGgtacccgcgtacgcgacgcccacccgccccccccccccccctgatccccttgcttgcttgtacaattttgcgattggcgcgcgtcgtgatgtcgcgtcgg

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G473906_T03 (Zea mays), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaa--caaagaattctctctttccctcttttctcatctcaaattccttctt---tctatggtggtggtgttcttcccggacggatggaactctag----
|||||| || |||||| | |||||| ||||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| | ||||||| | | | || |||| | | || || || | | | | | | | || |||
CGTCGGCAAGTCCAACATCCTCTCCCGATTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTGCAGgtaaacccacccgcaatgatttgaagaacgttctagtttataagtcgttttgacatttgtaaatacacaacttctgttatgtaactagacaaatagtgta

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G154960_T01 (Zea mays), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgta---acaaagaattctctctttccctcttttctcatctcaaattccttctttctatg---gtggtggtgttcttcccggacggatggaactctag---
|||||| || |||||| | ||||| |||||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || |||| | |||||| || | | ||| | | ||| ||| | | | ||| | |||| | | || | |||| | |
CGTCGGCAAGTCCAACATCCTCTCGCGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCTACCCGCAACCTGCAGgtacccccatacatacacctcaacaaccccgatctgatcgcgccccaatgtgccccatgcgcggcgtggccatttgccgccgtgcatggcgcgtctgttt

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G144008_T01 (Zea mays), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtg-gtggtgttcttc----ccggacggatggaactctag-----
|||||| || |||||| | || ||| | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||| | | | | ||||| |||| | | || | | | | | ||| | | || | ||| || |
CGTCGGCAAGTCCAACATCCTTTCCCGGTTCACCCGCAACGAGTTCTGCCTCGAGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCCTCCAGgtaa-gcccactccctccccgccctcgaatctctccctagatgagggagtcgagagatttattgcattcggcgggttcatactgctggggctggggcgttt

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA16G00350.1 (Glycine max), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttt------------tctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctag
|| || |||||||| | || ||| ||||||| ||||||||||| |||||||| ||||| ||||| || || ||||||||||| || ||||| | ||||| | || || | | || | | | | | | | || ||| || | ||| | | || | | |||
TGTTGGAAAATCCAATCTTCTGTCCCGATTCACTCGCAACGAGTTTTGCCTCGAATCCAAGTCCACCATTGGAGTCGAATTCGCCACTCGCACTCTTCAGgtcattaatttctcccagatctgatcaatagatgatggatatataacataattctactccttcgcatcattgtgataagttacctagcttagct-atttct--

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA12G28660.1 (Glycine max), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaattc--cttc---tttctat-----ggtggtggtgttcttcccggacggatggaactctag
|| || |||||||| | || ||| ||||||| ||||||||||| |||||||| ||||| ||||| || || ||||||||||| || ||||| | ||||| | | | || ||| ||||| ||| || ||| | | | || | | | | || |
TGTTGGAAAATCCAATCTCCTGTCCCGATTCACTCGCAACGAGTTTTGCCTCGAATCCAAGTCCACCATTGGAGTCGAATTCGCTACTCGCACTCTTCAGgtctttcttttcttccagatctgatcaagagatgtctggaattctactttgatttcctacccctcgctcgcatcattgtgcttacctagctattaccttt-

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA12G06280.2 (Glycine max), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccgga-cggatggaactctag-------------
|| || ||||||||| | |||||||| ||||| || ||||||||||| | |||||||||||||| ||||| || || ||||| || | || | |||||| | | ||| || | || | | | | |||||| | ||| ||||| | | | | |||| | |
TGTAGGCAAATCCAACATCCTCTCCAGGTTCACTCGAAACGAGTTCTGTTTGGAGTCCAAATCCACTATCGGAGTTGAGTTCGCCACCAGAACTCTTCAGgtag-atatgcttccctttactttgctgatttttttcaagattcctaagaaattcttcggt----ttcttgcggaagcagatgattattcatctgctcgtagtga

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA11G14360.1 (Glycine max), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaaga--attctctctttccctct------tttctcatctcaaattcct--tctttctatggt-ggtggtgttcttcccggacggatggaactctag
|| || ||||| ||| | |||||||| ||||| || ||||||||||| | |||||||||||||| ||||| || || ||||| || | || | |||||| | || || |||| ||| | ||| | | || | | ||| || | | || | ||| || |||| |
TGTAGGAAAATCTAACATCCTCTCCAGGTTCACTCGAAACGAGTTCTGTTTAGAGTCCAAATCCACTATCGGAGTTGAGTTCGCCACCAGAACTCTTCAGgtagttatacttatgcttccttttcctttgctgatttttccgtagtgaacgcatgtgcttgtgctgatcgaccgtttgctttttagatttctggattttg--

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT1G09630.1 (Arabidopsis thaliana), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgta-acaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctag--------
||||| || || || | ||||| |||||||| ||||||||||||||| | || ||||||||||| || || ||||||||||| || || || |||| ||| || | | ||||||| | | | | | | ||| || | | ||| | ||| | | | |
TGTCGGCAAGTCTAATCTCCTCTCTAGATTCACTCGCAACGAGTTCTGCTTAGAATCCAAATCCACCATTGGTGTCGAATTCGCTACTCGTACTCTCCAAgtacgcacacatctctctctatatatatagtatatagtgtaatcgaaatgttgctggatctaggtttagttctaagttaagcagcatccggtgcttttcg

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT1G07410.1 (Arabidopsis thaliana), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtgg--tggtgttcttcccggacggatggaactctag-------------
|| || ||||||||| | ||||| ||||||| | ||||||||||| ||||| ||||||||||| || || ||||||||||| || || || | ||||| | ||||| | | || ||| | | | ||| || | ||||||| | || |
TGTTGGTAAATCCAACATTCTCTCTCGATTCACCAGAAACGAGTTCTGTCTCGAATCCAAATCCACCATTGGCGTCGAATTCGCCACCCGGACTTTACAGgtcat------ctctcttctctcgctttctctaaatctagacaatttccctccagatcaatttggtgtttaatcttagattgtgtcgtcgcatttgcatcctctga

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv12s0035g01140.t01 (Vitis vinifera), 5'ss of exon 1
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttttctcatc-----tcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctag-----
|||||| ||||||||| | |||||| ||||||| ||||||||||| || | ||||| || || || ||||| || |||||||| || ||||| | ||||| | | || | ||| | | | | | || ||| || || ||| | | ||||| | || | |
CGTCGGCAAATCCAACCTCCTCTCCCGATTCACTCGCAACGAGTTTTGTTTGGAGTCTAAGTCTACTATCGGCGTTGAATTCGCCACTCGCACACTTCAGgttgctatctataca-tctgtacatacatacacactgtcagtcatatgttttgtttttgaatttagtgtgtttggtgtgtgtttatttgatttggagtgat

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S157_53V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctcttt----tctcatct-caaattccttctttctatggtggtggtgttcttcccggacggatggaactctag----
|||||| || || ||| | || |||||||| || ||||| ||||||||||| ||||| |||||||| ||||| || || || || || || | || |||||| ||||| | ||| || || | | | | | || || | ||| || | | || | |
CGTCGGAAAGTCTAACCTTCTTTCCAGATTTACACGCAATGAGTTCTGCCTGGAGTCGAAATCCACTATCGGTGTGGAGTTTGCTACTCGTTCCATTCAGgtattttcccgctctcttcgtaatattttgaattccaatttatgagaccggttaattggtgatgagaatacgtttcaaagattgctcgatttatgataat

upper sequence: EFJ06060 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S209_94V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaagaattctctctttccctc--ttttctcatctcaaa-ttccttctttctatggtg------gtggtgttcttcccggacggatggaactctag
|| ||||| ||||| |||| |||||||| ||||| |||||||||||||| ||||| || || || || || || || || || || || | ||||||||| | | || | | | | | | | || | || ||| || | | | | | || | || | |
TGTGGGGAAGTCCAATCTGCTTTCCAGATTTACGCGGAACGAGTTCTGCCTGGAGTCGAAGTCGACCATTGGCGTGGAGTTTGCCACTCGATCTATCCAGgtatcgtccggcccgtgctggcatgcaatgtcgtgagggcggggtttggtgcggctgcggtcgaagctgtagaggtgtgactagaagcgagggtccgggg

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: 7

CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaaga ... ggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC




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