Sequence
atgc intronic sequence ATGC exonic sequenceAAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgtattctctttttgcttgcaaagccctcttgatgattttggaaacttggcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ20945 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G337819_T01 (Zea mays), 5'ss of exon 10
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgtattctctttttgcttgcaaagccctcttgatgattttggaaacttggcag-------------------------------
| | || |||| || ||||||||||||||||||||||||||||| || | | | || ||||| | | | ||| ||| ||| || || |
ATGAAGGTGAGGTATTCTGCTGGGGATGGAACAAGTATGGCCAGgtgggtgccccttaacatacctt--ttgcataaacatattgga----ttgtaaaattagctgtggtctatcgaatctgtggtcgtttatgcag
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G302245_T01 (Zea mays), 5'ss of exon 8
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgt--attctctttttgcttgcaaagccctcttgatgattttggaaacttggcag-------------------------------
| | || |||| || |||||||||||||||||||| |||||||| | ||||| | | | | || | | | | | | | || ||| ||| || | |
ATGAAGGCGAGGTATTCTGCTGGGGATGGAACAAGTACGGCCAGgtgactagctcttaacatacctcttacatatatatgcatatcgaa----ttgtaaaattaactgtggcttatcgaatttgtgttggcttatgcag
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA18G03870.1 (Glycine max), 5'ss of exon 10
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagta-gctgtatt-ctctttttgcttgcaaagccctcttgat----gattttggaaacttggcag-----------------------------------------------------------------------------------------------------------------
| || || || || || ||||||||||||||||||||||| ||||| || || ||| | ||||| || ||| || || ||||| | | | |
ATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAGgtgcttatattgcattaccatttttatgtgtc---tccttttaatttcatattttaaacaatcaatattgttgaaatttctatctgaccattgcatattttagctgatacttgttttttgaattgttggcattcttggtactgaacatactattctaagttttaatttctgaatgtgacag
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA11G34470.1 (Glycine max), 5'ss of exon 10
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagta-gctgtattctctttttgcttgcaaagccctcttgatg-attttggaaacttggcag--------------------------------------------------------------------------------------------------------------------------
| || || || || || ||||||||||||||||||||||| ||||| || || | | | |||| | || || | | | | || || || |
ATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAGgtgcttatattgcactaccatttt-catgtgtctccttttaatttcacatttaaagtttaaacgatcaatattgctgaattttcaatctgaccatatgcatattttaagtgatactcattttgtgaattgttggcgttcttggtactgatcatactattctaaatttcaatttctgaatgtggcag
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 5'ss of exon 10
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgtattctctttttgcttgcaaagccctcttg----atgattttggaaacttggcag-----------------------------------
| || | ||||| ||||||||||||||||||||||||||||| || | || || | | | | || | | ||||| ||
AGGGAGGAGAAATTTTTAGCTGGGGATGGAACAAGTATGGCCAGgtatgt--ttataatcctgatcaatctagggaacgctttcactataccattttttcttttttcttttcttctcatggaaggttttctcgctctgtatgcag
upper sequence: EFJ20945 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 5'ss of exon 10
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgtattctctt---tttgcttgca---aagccctcttgatgattttggaaacttggcag--------------------------------
| || || | || | ||||||||||||||||||||| |||||| ||| | ||| ||| | || | | || | ||| | ||| |
CCGATGGAAAAATGTTCTCCTGGGGATGGAACAAGTATGGTCAGgtataatgctcaaactgcttatatttatctacatctgggtgcatttagacaccatgggacattgaaatcactctgtattgtgttaatctatttgaaattaMapped 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|169025411|gb|FE436025.1|FE436025EST: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAG CTAGGACTTGGCGACACGGGCGACCGTGATAC
genomic: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagct ... aacttggcagCTAGGACTTGGCGACACGGGCGACCGTGATAC
EST:
gi|169082715|gb|FE486222.1|FE486222EST: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAG CTAGGACTTGGCGACACGGGCGACCGTGATACTCCTCATGAAGTTCCGCTC
genomic: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagct ... aacttggcagCTAGGACTTGGCGACACGGGCGACCGTGATACTCCTCATGAAGTTCCGCTC
EST:
gi|169061306|gb|FE470393.1|FE470393EST: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAG ---G-ACTTGGCGACACGGGCGACCGTGATACTCCTCATGAAGTTCCGCTC
genomic: AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagct ... aacttggcagCTAGGACTTGGCGACACGGGCGACCGTGATACTCCTCATGAAGTTCCGCTC
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:
22AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagct ... aacttggcagCTAGGACTTGGCGACACGGGCGACCGTGATACTCCTCATGAAGTTCCGCTCGAGCACCGGGCAGTAAACGTAGCGTGTGGGTGGTGGCATACTCTCGCGC
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Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAAGGGGAAGGTTTTTTGCTGGGGATGGAACAAGTATGGCCAGgtaagtagctgtattctctttttgcttgcaaagccctcttgatgattttggaaacttggcag
- - - - - - - - - - - - GATGGA