Sequence
atgc intronic sequence ATGC exonic sequencegtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ15163 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttgg----cagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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-------------gtactgcctcccacccgctaaaaccctagctttcttcttcctcgattcggtttgctccctcgcgctaatcccgctcgatttcgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G307906_T01 (Zea mays), 3'ss of exon 4
--gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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gtaacccgccctaaaccctagcttcctcttcgaactcgcttactcgcacccggatcgattcgcctcgatctatg-cgctgattctgcttt----tttgtagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAATGAGGGGAACTACCTGGCCCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGCGCC
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G100620_T01 (Zea mays), 3'ss of exon 1
--gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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gtaacccgccctaaaccctagcgtactcttcga----actcgcccccgt----ctcgattcgcttcgatctatg-cgctga--ttctgattgttt--gtagCTATGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTAGCCCACACGCAAGGGAAGAGGCACCAGACCAACCTCGCCAAGCGCGCC
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G32600.1 (Arabidopsis thaliana), 3'ss of exon 1
gtctgtctctctttcatttttttctcttggaggagaatgtccgctgt--ttttctcgagattgggcgagtgatggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
|| | | ||| | || | ||| | | || | | | | ||||| | || | | | ||| | ||| || ||||||| |||||||| || || | || ||||| |||||||| ||||||||||||||||| || ||||| ||| | || ||||| || ||||| ||| | ||
-cttgagtttgtttggctgttgtttctagaattaggttcttttttttaattttcccctcatgccactaatttgatttttggtgtgtttttatgttgtgcagCTATGAGTGTAAACTATGTCTAACACTGCATAACAATGAAGGAAACTACTTGGCACATACTCAAGGTAAGAGGCATCAGACAAACTTGGCAAAGAGAGCT
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
----gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaat-tcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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cagaaaataaccctatatatatatactccattctatttggatctc-gctattttattttatttt---tttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
upper sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
gtctgtctctctttcatttttttctcttggaggagaatgtccg-ctgtttttctcga--gattgggcgagtga--tggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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atgtgtacggatattgtccctttctctttgtactgcatggaaggtcatttcactggaacgattatcttattgaaatatagtgggtatttccttggt----gcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCAMapped 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|169113992|gb|FE516463.1|FE516463EST: ACGATCGACCTGGGCAAGGATCCCTACTTCATGCGCAATCACTTGGGAAG CTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTT
genomic: ACGATCGACCTGGGCAAGGATCCCTACTTCATGCGCAATCACTTGGGAAGgtctgtctct ... gttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTT
EST:
gi|169061018|gb|FE470648.1|FE470648EST: ACGATCGACCTGGGCAAGGATCCCTACTTCATGCGCAATCACTTGGGAAG CTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTT
genomic: ACGATCGACCTGGGCAAGGATCCCTACTTCATGCGCAATCACTTGGGAAGgtctgtctct ... gttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTT
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:
34 (upstream exon),
31 (downstream exon)
Score:
8AGAATGAGGCGATCGATAGGCGCGAGCGTCTCCGGCGCCTCGCCATCGAGACGATCGACCTGGGCAAGGATCCCTACTTCATGCGCAATCACTTGGGAAGgtctgtctct ... gttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttttctcgagattgggcgagtgatggcattgaaattcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG
attgaaatt TA-rich tract