Sequence
atgc intronic sequence ATGC exonic sequencegtccgtgatctttctttcttcttcttgaagtttccagattgctcactggcttttcttttcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ18860 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S321_33V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------------------------------------gtccgtgatctttctttct-------tcttcttgaagtttccagattgctcactggctt--ttcttttcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
| | || ||| |||| || | | || | | | | | || | || | | |||||||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||| | || || || ||||| || || | |
gtataacttgtgctcgggacgttcttgctacaaatagatctgttcgatagaaatatttttttcgaagcttgtcgtgtgagagctgcaacagctaaccttgatctaattggtggattgtacagACTGCTTTCACAACCCAGAAGGACTTCGGAAAAGAGGCACGTGAAGCCCAATGGGCTCATGCTCAGCGGACATTGCATGGACTGCATCCTCCCCAATCTA
upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S133_22V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------------------------------------------------gtccgtgatctttct--ttcttcttcttgaagtttccagattgctcactggcttttcttttcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
| ||| |||| | | ||| || | | | ||| ||| || | || | | |||||||||||| |||||||| |||||||| ||||||||||| ||||||||||| ||||| | || ||||||||| | || || ||||| || || ||| | |
gtacgaccttttccttcgtgctcatgaagcggtagtgtctattccacctttgctctgaccagtggactttataataattcatcaacgaagtacgtgatggcttacc--ttattggtgggttgcacagACTGCTTTCACAACCCAGAAGGACTTCGGAAAGGAGGCACGTGAAGCTCAGTGGGCCCTTGCCCAGCGAACATTGCATGGACTCCACCCTCCCGAATCCA
upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S6_11V6.1 (Physcomitrella patens), 3'ss of exon 16
----------------gtccgtgatctttctttc-----ttcttcttgaagtttc-cagattgct--cactggcttttcttt-----tcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
| | | | | || || |||| ||| | | | | |||| | | | ||||| || || ||||||||| || ||||| || || ||||| |||||||| || ||||||||||| ||||||| |||||||||||| | || || || ||||| || ||| | |
gtacagttttctctctctacatcaaccttgttctggaaattctgcttcgaataacacggattcatgctattaacttttattcattgatctgtcacagACTGCGTTCACAACTCAGAAAGACTTCGGAAAGGAAGCTCGTGAAGCTCAGTGGGCTCTCGCTCAGCGAACCTTGCATGGACTACATCCTCCTGAATCCA
upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S321_30V6.1 (Physcomitrella patens), 3'ss of exon 16
-----------------------------------------------------------------------------------------gtccgtgatctttctttcttcttcttgaagtttccagat-----tgctcactggctttt-cttttcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
|| || | | || | ||| ||| ||| | | | | | ||||||| || || || | || ||||||||||||||||| || || ||||| || ||||| || || ||| ||||| | |||||||| |||||||||||| | |
gtatgattaattcatgtatttaggatatatatatatatatatatatatatatatatatatatattttcgtatgttgccgcactgatagtgttgaagaattggaatgggcaatcggataacaatgagacaataatgcatcgtggttgtggccctccttaaacagACGGCATTCACGAGGCAGAAGGACTTTGGAAAGGAAGCTCGGGAAGCGCAGTGGGCGCATGCACAGAGAACATTGCACGGGCTGCATCCACCGGAATCCA
upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S137_291V6.1 (Physcomitrella patens), 3'ss of exon 18
----------------------------------------------------------------------------gtccgtgatctttctttcttcttcttgaagtttccagattgctcactg----gcttttcttttcacgaa-cagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
| | | || | | | || |||| | || | || || | | || ||||| || || || | || ||||| ||||| || ||||| ||||||||||||||||| || |||||||| ||| | || || ||||| || | ||| |
gtttgtgttcgcacttctagataaaaagagaataacatctttaagattaaaatgaaaaattgatcctcggtagtaacttaaaaacttaaattacatttggaccggattagtgagatgcttattgtttgggttgtcaatctatgattcagACCGCCTTCACTAGACAGAAGGATTTTGGGAAAGAGGCGCGTGAAGCTCAATGGGCCCATGCTCAGCGCACATTGCATGGACTCCACCCTGCCGAATCCGMapped 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|169113424|gb|FE514751.1|FE514751EST: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAG ACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAA
genomic: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAGgtccgtgatc ... tcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAA
EST:
gi|169061704|gb|FE469894.1|FE469894EST: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAG ACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAGGCTCAA
genomic: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAGgtccgtgatc ... tcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAA
EST:
gi|169045922|gb|FE451232.1|FE451232EST: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAG ACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAGGCTCAA
genomic: TGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAGgtccgtgatc ... tcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAA
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:
115GCTTTACAGTCTCGTAACTTACATCCCTCTAGACTTCCTAAAGATCTTCGTGCGTTACGTGCTAAGCGGCAAAGCATGGCAGAACATGATCGAGAATAAGgtccgtgatc ... tcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcttcttcttgaagtttccagattgctcactggcttttcttttcacgaacagACTGCTTTTACAACCCAAAAGGACTTTGGAAAGGAGGCCCGTGAAGCTCAATGGGCTCACGCTCAGCGAACACTCCACGGGCTCCATCCACCGGAAACAA
tgctcac putative branch site (score: 115)
ctggcttttcttttc CT-rich tract
ttttctttt TA-rich tract