Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ08612 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 4
---------------------gtaagtggtgaattctctttctttctcagcctggggtgc------tgattcggatt--gtttt--------cttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
| | || || |||| | | |||| || | | ||| | || || | |||| | | ||| ||||| || ||||| || | || |||||||||| |||||||| ||||| || ||||| ||||||||||| || ||| |||||||
gtaagcattactttcatattcgctttctctctccctcctctccctctctgtcatttgtgcatacattgcatggaatttgatcttacagatgatttttgcagCATCATTCTTTATATCTGTCTACTATGCCTATCAACGAACGTGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCAT
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
--------------------------------------gtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
|| | || || || || | || | | || || | |||| | | ||| || | || ||||| || | || | |||||||| |||||||| ||||| || ||||| ||||||||||| || ||| ||||||
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------gtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
||||| || || | || || | || || || || || || || ||| | |||||||| ||||| || ||||| | | | || | ||||||||||||||||||||||| |||||||| ||||| ||||| || ||| |||| ||
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttg------tggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
|| | | | | | || | |||| || |||| | |||| | |||||||| ||||| |||||||| ||| | || | ||||||||||| ||||| ||||| || ||||| |||||||||| |||||| |||| ||
gtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaa--tgttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------gtaagtggtg-aattctctttctttctcagc---ctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
| | ||| || | ||| | || |||| || | || || | || || | ||| ||||| | || || ||| || || | || | |||||||||||||||||||||||||||||||| |||||||||
gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggctgttttatttcatcatttttcgtgtaagtgcagttcataagcacttcgctggagtaataatgaggttc--ttgtttgtgcagGCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG-----------------
upper sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------gtaagtggtgaattctc-tttctttctcagcctggggtgctgat-tcggattgtt-----ttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
|| || ||| | | ||| ||| || | ||| | | | | || || | | |||| ||||| | || || || | || || | |||| | ||||||||||||||||| |||||||| ||||| ||||| ||||| | | | |||| |
atcacttcgtcagtgtatctcttgcttatgtttgtaaggaagtaccgttttacaagcagtggcggctactgttcttacactattgtcgcctcatttgcagCTACATGGGCAGTATCGGTGTACTTCGCATATGCGCGGACCTGGAAGCCTTTCAATCCCATTCTCGGTGAGACCTATGAGATGGTCGACAAGAATGGCCTMapped 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|169060494|gb|FE469000.1|FE469000EST: GGACCTCGCTGATCAGTGCGAAGATCCATACTTGAGGATGGTCTATGCTT CGTGCTGGGCTATCTCTGTATATTATGCTTACGAACGTGC-GTGGAAGCCA
genomic: GGACCTCGCTGATCAGTGCGAAGATCCATACTTGAGGATGGTCTATGCTTgtaagtggtg ... tcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCG-GCCGTGGAAGCCT
EST:
gi|169025463|gb|FE436077.1|FE436077EST: GGACCTCGCTGATCAGTGCGAAGATCCATACTTGAGGATGGTCTATGCTT CGTGCTGGGCTATCTCTGTATATTATGCTTACGAACGTGC-GTGGAAGCCA
genomic: GGACCTCGCTGATCAGTGCGAAGATCCATACTTGAGGATGGTCTATGCTTgtaagtggtg ... tcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCG-GCCGTGGAAGCCT
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:
31 (upstream exon),
33 (downstream exon)
Score:
30TTGATGGAGTATGCACACCTTTTGGACCTCGCTGATCAGTGCGAAGATCCATACTTGAGGATGGTCTATGCTTgtaagtggtg ... tcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
tgctgat putative branch site (score: 30)
ttgttttcttctac putative PPT
attgtttt TA-rich tract