Sequence
atgc intronic sequence ATGC exonic sequencegtaaagctctcgtgcctttgtcaccttgcgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ20301 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------------------gtaaagctctcgtgcctttgtcaccttgcgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
| || | | || | | | | || | | | |||| ||||| | |||||||||| || ||||| ||||| || ||||| ||||||||| | || ||||||||||| ||||| |||||
gtaggaatttacacatgatccttattaccgcactcatgggcaccttactctattgatgttttccagcaaaaatgaaacatgtcaacttatttcaagcttgctatatatttactcccaagtactaacattgtttgactgcaccgaacaatttgtgcatgacacttgtatgacagGCAGAGTCATCGCCGAGAGTGTGATATATAGCTATGGAACAGTTCTTTTGGATCTTTTGAGTGGGAAGCACATACCTCCTAGCCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 5
---------------------------------------gtaaagctctcgtgcctttgtcaccttg---cgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
|| || | | || | ||| | | | || ||||| | | |||| ||||||| ||||||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || ||
atctattgtttcgtttaagtttacaatacactattcacactattactgtttacaatatgctattttggactgcactgaataatttgtgcttgaatgacagGCAGAGTAATTCCCGAGAGTGTGATATATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 5
---------------------------------------gtaaagctctcgtgcctttgtcaccttg---cgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
|||| || | | || | ||| | | || ||||| | || |||| ||||||| || |||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || ||
gtctattgttttgttcaagtttacaatacactattcacagtaatactgtttacaatatgctattttggactgcgctgaataatttgtgcttgcattacagGCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 5
-----------------------gtaaagctctcgtgcc------tttgtcacct-tgcgtattcaaagctttgttttc------------tgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
| | || || | |||| || || | || | | | | | | |||||| || ||| || |||||||| || || |||||||| |||||||| |||||||||| || || ||||| ||||||||||||||
tacctgatattccattgtttgtttcagaactgtcttattagaagttttgccaactataattaatgataatatgatacttaacaaataacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 5
------------------------------gtaaagctctcgt-------gcctttgtcaccttgcgtattcaaagctttgttttc-----tgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
| | || || | | ||| | || | || | | | | | | |||||| || ||| || |||||||| || || |||||||| |||||||| |||||||| | || || ||||||||||||||||||||
attgttttacctgatgttccattgattgtttcagaactgtcttattagaagtcttgctaactataattaatgacaatatgatacttaacaacacctgcagGCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTTTAAGTGGCAAGCACATTCCTCCAAGCCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G50990.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------gtaaagctctcgtgcctttgtcaccttgcgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
| | | | ||||| | || || | | | | | | ||| ||||| ||| || ||||||||| | | || | ||| || |||| |||||||||||||| ||||| |||||||||||||| ||
tgtattgcccttaaaacgttaatatatgaatgatgtgataatggttcattataagacttttgtgcctttttgtggcacatgatgtatataaatattgtagGTACGTTAATTCCAGAGAGTGTTGTCTTCAGCTTTGGGACGTTTCTTTTGGATCTTCTTAGTGGGAAACACATTCCTCCAAGTCAT
upper sequence: EFJ20301 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------------------------------gtaaagctctcgtgcctttg------tcaccttgcgtattcaaagct-ttgttttctg-tttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
||||| | || ||| | || ||| | | | |||| ||| ||||||||||| || ||||| || ||||||||||| || ||||| |||||||| | ||||| | || |||||||| | ||||| || |||
gtaccaacttggcatacacccccccatgagtacttaagaactggtaacgaagtctgaagcttggtaatgtatttgcgcaattctggacattattacggacctacccaaaattaccaacattcaaagcagccctggatttagtatgcttactttggattcctgagattcttgtattcaaatttgcagGTAGGGTGACACCTGAAAGTGTTATTTACAGCTATGGAACTGTTCTACTAGATCTGTTGAGTGGGAAGCATCTACCTCCTAGTCACMapped 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|169075974|gb|FE480982.1|FE480982EST: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAG GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
genomic: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctct ... ctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
EST:
gi|169097974|gb|FE498771.1|FE498771EST: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAG GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
genomic: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctct ... ctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
EST:
gi|169102668|gb|FE504461.1|FE504461EST: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAG GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
genomic: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctct ... ctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
EST:
gi|169082053|gb|FE490565.1|FE490565EST: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAG GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
genomic: GAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctct ... ctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGG
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:
33 (upstream exon),
35 (downstream exon)
Score:
17GATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctct ... ctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagctctcgtgcctttgtcaccttgcgtattcaaagctttgttttctgtttgcagGTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC
ctttgttttctgttt CT-rich tract
tattcaaa TA-rich tract