Sequence
atgc intronic sequence ATGC exonic sequencegtgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ13375 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os01g51380.1 (Oryza sativa), 3'ss of exon 13
-------------------------------gtgagcgattgtgtctacatcattatgc----cgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
| | | | | | | ||| |||| | | | |||| ||||| ||||| || || ||||| ||||| ||||| || |||||||| || || || ||||| |||||||||||||| || || |||
gtcggttgggcgttcatagcctatgttctgcacaaactaccttaaccaagtatatatatggagtatttactcggatgtgtttgttt--cagCTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
-------------------gtgagcgattgtgtctac-atcattatgccgt-ttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
| | | | | | | || ||| | ||| ||| | | ||| |||||||||||||| ||||||||||| || || || || || ||||||||||| || ||||||||||| || |||||||| || |||
gtctggttttgcttgtttactacattgctattttttctgtttataagccatcttattggtgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 13
-------------------------gtgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG-
| | || ||| || | | || | || | | | | ||| ||||||||||||| ||||||||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||
tctggttttgcctgcttaccacattgctattttttctgtttataa-accatctcatt-ggtgttattttgtttcttttaagcTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
------------------------gtgagcgattgtgtctacatcat-tatgccgt----ttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
|| | | | |||| | | | || | | | | |||| |||||||||||||| ||||| ||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------gtgagcgat-tgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
|| | ||| || | || || ||| | || | ||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || || ||||||
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------gtgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGG-GAGAAGAAGC-GCTGTCATCTGAAGATCTG----------------------------
| | | | | |||| | | | | | || || | | | || | ||| || ||| | | | | | | || | | || | | ||| | ||||| | | ||
gttagaattcaactccattttgattaatacccattgcattctatctccagatcttattaacgtattgtttctcattctgttagA-GTGCTATCGGCGAGGGCAT--GACTCGTAAAGACCATTCTGATGTGTCGAACCAGCTGTATGCAAATTATGCAATCGGGAAAGATGTTCAAGCGATGAAAG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
---------------------gtgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
| | | | | | || | || ||| | | | | || |||||||||||||| ||||| ||||| || || |||||||| ||||||||||| || ||||||||||| || || ||||| ||||||
gtagtatttgatgttcgggctgcgttcaccttctctttgagcac-gtcccaactaatgcgattc-ttcttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
------------------------------------------gtgagcgattgtgtctacatcatta--tgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
| | || | | || | | | ||||| | | | | ||| | ||||| || ||||||||||| || || |||||||| ||||| |||||||| ||||| ||||| |||| || |||||||||
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG
upper sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------gtgagcgattgtgtctacatcattatgccg--tttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
||| | | || | ||| | | ||||||| || | |||||| | || ||||||||||| ||||| || || || ||||| ||||| ||||| |||||||||||||| |||| || || ||||||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtcaagactttgggtttaacatggtgtctacccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGMapped 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|169083324|gb|FE491368.1|FE491368EST: CTATTGGAGAAGGTATGACCCGAAAGGATCACTCCGACGTTTCGAACCAG CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTC
genomic: CTATTGGAGAAGGTATGACCCGAAAGGATCACTCCGACGTTTCGAACCAGgtgagcgatt ... ggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTC
EST:
gi|169083325|gb|FE491369.1|FE491369EST: CTATTGGAGAAGGTATGACCCGAAAGGATCACTCCGACGTTTCGAACCAG CTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTC
genomic: CTATTGGAGAAGGTATGACCCGAAAGGATCACTCCGACGTTTCGAACCAGgtgagcgatt ... ggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTC
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:
30 (upstream exon),
28 (downstream exon)
Score:
9AGTGCTATTGGAGAAGGTATGACCCGAAAGGATCACTCCGACGTTTCGAACCAGgtgagcgatt ... ggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
gtttaac putative branch site (score: 9)
atcattat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcgattgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA