Sequence
atgc intronic sequence ATGC exonic sequencegtgagcgagcgtcttgtctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ26636 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S47_42V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgctt----ctcgtgttctaaacttctctcgcctctggtgac--gcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
| | | | | | | | | || || | ||| | | | | || | ||||||||||||||| |||||||| ||| ||||||||||||||||||||||| || |||||||| | |||||||| || || || ||||| || | ||||
gtaataagaattttccactctttcggaagtctaaacccggttcaattagattctttcatggtgatgtgatcaggattgttaattttggttttggtctcgaaggtgttttcccttttttcatttttaaatcttttattcaagagtattaatcatggtgtttctttgcagCCCGAGATGATTGGACACTATTTGGCTGAGTTCTCCATCTCGTACAAGCCCGTAAAGCACGGTAGGCCCGGTATTGGAGCTACCCACTCTTCGCGATTTA
upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S91_124V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtgagcgagcgtcttgt-ctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | | || || | ||| | | | || | ||| | |||||| |||||||| || |||||| ||| ||||||||||| ||||||||||| ||||||||||| | |||||||| || || || ||||| || | || |
gtataatattcggtcacgctatttttgactctccatcagtccgtgctatagggaagaattgattgaattcaatactagcttggacaacggagtagagggtggactggttccatttgcagcgtgaaagcctgaccttgtaaatgtct--ttgtgcagCCTGAGATGATTGGGCACTACTTGGCTGAGTTCTCCATTTCGTACAAGCCTGTCAAGCACGGTAGGCCCGGTATTGGAGCTACGCACTCTTCGCGATTCA
upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S13_413V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgctt------ctcgtgttctaaactt--ctctcgcctc-tggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | | ||| | || | ||||| || || | | || | || |||||| |||||||| ||||||||| ||| |||||| ||||| ||||||||||| || ||||| || | ||||||||||| || || ||||| ||| | ||||
gtatagtgaatctatgcctttttcattaatgatcccatttggcatcaaacacattttatcaatgtggacatcgacaactgtcggaagttctgcgcatccctggtttgggttgttgaagaaaagattagagacttgaagttctgaatttaattttgatttcgttgttttgcagCCTGAGATGATTGGACACTACTTGGCAGAGTTTTCCATATCGTACAAGCCTGTGAAGCATGGTAGGCCCGGTATCGGAGCTACCCACTCCTCCCGATTTA
upper sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S223_96V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------gtgagcgagcgtcttgtctgcgtgcttc----tcgtgttctaaacttctc-----tcgc-ctctggtg-----acgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
|| | ||| || || | | || | || | ||| || ||| || | || || || ||||||||||||||| |||||||| ||| || || ||||| ||||||||||| || |||||||| || || |||||||| || || ||||| || | || |
gtaataatatatttattatgatcgacccagtagtctgaaaattcttgatgaagagtagttcatcctgtgagagtatcccctccccctagtttggcatggttatataatctactcaggattctcactttgatgtttccgtgcagCCCGAGATGATTGGACACTATTTGGCTGAATTTTCCATTTCGTACAAGCCTGTGAAGCACGGTCGGCCTGGTATCGGAGCTACCCACTCTTCGCGATTCAMapped 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|169097202|gb|FE497124.1|FE497124EST: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
EST:
gi|169027972|gb|FE435889.1|FE435889EST: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
EST:
gi|169074868|gb|FE482749.1|FE482749EST: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAG CCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
genomic: GCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCA
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),
31 (downstream exon)
Score:
61AGTGCGAACGCATCTCCGGAGCATGATCATCGTCCCAGAGATGATTGGCAGCATCATTGGCGTCTACAACGGCAAGACGTTCAACCAGGTGGAGATCAAGgtgagcgagc ... ggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtcttgtctgcgtgcttctcgtgttctaaacttctctcgcctctggtgacgcagCCCGAGATGATCGGACACTACCTGGGAGAGTTCTCCATCTCGTACAAGCCAGTCAAGCACGGGCGTCCCGGTATCGGTGCCACACACTCGTCCAGGTTTA
ttctaaa putative branch site (score: 61)
cttctctcgcctctg CT-rich tract
ttctaaa TA-rich tract