Sequence
atgc intronic sequence ATGC exonic sequencegtcaggctctttctctgttctctctcgtctctgaaaatcctcctccatttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31330 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ31330 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g30170.1 (Oryza sativa), 3'ss of exon 4
---------gtcaggctctttctctgttctctct-cgtctctgaaaatcctcctcc-----atttgcta-----gAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
|||| | | | | | |||| ||||| | || | | | ||||| ||| || ||||| | || || || ||||| |||||||| ||||| ||||| || ||||| || |||||||||||||| || || ||||| || |||| |
gtatgtgcaatcagtacatatttatttcctctggatatctctaagcatttccggtctaacaaaatgctactttagAATCACATCCCAAGAGTCGGTGATTTCAATGAGAGCACATACTATATGGAGGGTAACACTGGGCATCCAGTGTTTGAAACAGCATATGGGAAAATCGGAG
upper sequence: EFJ31330 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G077673_T01 (Zea mays), 3'ss of exon 2
----------------------------gtcaggctctttctctgttctctc-tcgtctctgaaaatcctc-------ctccatttgc-------tagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
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gtatgtgtatcgctacaattttattttccttggctgcattttctatttcttcattctgtcagaaagcttttacattgtcttaataaacgctactgtagAATCACATTCCAAGAGTTGGTGATTTCAATGAGAGCACATACTACATGGAGGGTAACACTGGGCATCCAGTGTTTGAAACAGCTTATGGCAAAATAGGAG
upper sequence: EFJ31330 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA07G30090.1 (Glycine max), 3'ss of exon 4
-----------------------------gtcaggctctttctctgttctctctcgtctctgaaaatcctcctccatttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
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gtaattgcctaagctctctgcttctaattttaatgccaaatagcttcccttttaccaatctcatgaacacataacatttggcagAACCATATACCAAGAGTTGGAGACTTCAATGAGAGCACATATTATATGGAAGGAAACACCGGCCACCCTGTATTTGAAACAGCATTTGGAAAAATTGCCA
upper sequence: EFJ31330 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G64370.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------gtcaggctcttt----ctctgttctctctcgtctctgaaaatcctcctccatttgct-------agAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
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gtatatttgtgctaacacgtcttttgttgctctgtcttttctcttgtcagctaatt-tctattacttgcttggtggcagAACCATATACCTAGGGTAGGAGATTTCAACGAGAGCACCTATTACATGGAAGGAGACACAGGCCATCCTGTGTTTGAGACGGTGTTTGGGAAAATTGCGG
upper sequence: EFJ31330 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: EDP09706 (Chlamydomonas reinhardtii), 3'ss of exon 5
-------------------------------------------gtcaggctctttctctgtt-ctctctcgtctctgaaaatcctc-ctccatttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
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tcgcacctgactttgaggaaaagaaacgcgcgctcgccagtgcaacggctcaacacgctgcggcgtacccgtgtgtgtgcgtgttcacgtcaccctgtagAACCACATCCCGCGGGTGGGCGACTTCAACGAGTCCACCTACTACATGGAGGGCAACACCGGCCACCCCGTGTTTGAGACGGCGTTCGGCAAGATCGCCGMapped 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|169034502|gb|FE444562.1|FE444562EST: CGGCCGTGGTGATTGGAAACAATGGAAACGTGATTGGAAAGCACAGAAAG AACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAA
genomic: CGGCCGTGGTGATTGGAAACAATGGAAACGTGATCGGAAAGCACAGAAAGgtcaggctct ... catttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAA
EST:
gi|169034501|gb|FE444561.1|FE444561EST: CGGCCGTGGTGATTTGAAACAATGGAAACGTGATTGGAAAGCACAGAAAG AACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAA
genomic: CGGCCGTGGTGATTGGAAACAATGGAAACGTGATCGGAAAGCACAGAAAGgtcaggctct ... catttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAA
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),
35 (downstream exon)
Score:
9CAGCCCCATCCTGGAGCGCGACGAAGTCCACGGTGGAACCTTGTGGAACACGGCCGTGGTGATTGGAAACAATGGAAACGTGATCGGAAAGCACAGAAAGgtcaggctct ... catttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaggctctttctctgttctctctcgtctctgaaaatcctcctccatttgctagAACCATATCCCTCGCGTTGGAGACTTCAACGAGAGCACGTACTACATGGAAGGCAACACCGGCCATCCAGTGTTTGAGACCGCGTATGGAAAGATCGCGG
tcctcctccatttgct CT-rich tract
tgaaaat TA-rich tract