Sequence
atgc intronic sequence ATGC exonic sequencegtaacaatcatcttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ33440 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------gtaacaatcatcttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
|| ||| || | | | || | |||| | | || |||| |||| ||||| || |||||||||||||| || |||| ||| |||||||||||| |||| | | || ||||||| ||| | || ||| | || || || |
gcatgacaacttcattcttttttggcagagttttattgtgaaaattgctgtctcactttgttgttgatcta-atggtgcacttgtttttggaacataaaagGGTGAGAAAGATGATAAGATCATCGCGGTTTGCGTTGATGATCCCGAGTTCCGCCACTTCAATGATCTCAAGGAGCTCTCTCCTCACCGACTTGCTGAAA
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 3
-------------------gtaacaatcatc-ttgctcttgtctgaa----tgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
|| |||| | | | | | ||| | | | | | || | |||| | | ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||||| | |||||| | ||||||| || ||| | || ||| | || ||||
gtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaat--tgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtaacaatca--tcttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
| ||| || | |||| || | | ||||||| || | | || | |||||| ||||| |||||||||||||| || || |||||||||||||| || | ||||||| |||||||| || || ||||| || || || || ||||
gtgatgtcatttctctcaagcaaatcatgcaaccattagttcttcacagtgagttgaggcatatgaaat-tcagttctttattcataccagGGAGAGAATGACGATAAGATCATTGCTGTATGCGCTGACGATCCAGAATATCGACACTACACTGACATCAAAGAGCTTCCACCTCATAGACTAGCTGAGA
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
| || | | || | | | | | | | |||| || ||| ||| |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| ||
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATCTGTT--CGGAATGC---AGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------gtaacaatcat---cttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
| || | | || | | | | | | | |||| || ||| ||| |||| ||||||||||| ||||||||||||||||| || ||||| ||||||| || ||| | | | |||||||| || || ||||| ||| | |||| ||||
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagcaacgtgagatctgtt--cggaatgc---agGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGAGCTTCCACCGCACCGATTGGCGGAGA
upper sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------gtaacaatcat--cttgctcttgtctgaatgcatatggaagattaa-ttggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
|| || | || | || ||| | || || |||| || || || |||| |||||||| || ||||||||||| || || ||||||||||| |||| | ||||| | |||||||||| || | || || || | || || || |
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAAMapped 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|169109380|gb|FE514104.1|FE514104EST: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAG GGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
genomic: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... actgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
EST:
gi|169029484|gb|FE436726.1|FE436726EST: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAG GGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
genomic: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... actgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
EST:
gi|169054473|gb|FE462154.1|FE462154EST: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAG GGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
genomic: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... actgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
EST:
gi|169095336|gb|FE499405.1|FE499405EST: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAG GGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
genomic: GATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... actgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTC
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),
29 (downstream exon)
Score:
33GAGCCTGTGTTGCCTGGATGCTTTCTGCGAGCGAGAGCGATTGGACTGATGCCGATGATTGATCAGgtaacaatca ... actgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcatcttgctcttgtctgaatgcatatggaagattaattggtggactgctccagGGCGAGAAGGACGATAAGATCATCGCCGTGTGCGCTGACGATCCCGAGTTCACACACTACCAAGACATCAAGGATCTCCCACCCCACAGGCTGGCAGAGA
gattaat putative branch site (score: 33)
ctgctcc putative PPT
aagattaatt TA-rich tract