Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaattttctttcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ38338 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
------------gtaagaaattt--tctttcttactcttgaaggctcgtgttcttgg----------gtctaaacacttcttacttt--gtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
| | |||| | || || ||| | || | | | | ||| || || ||| | ||||||||||||||||| ||||||||||| || |||||||| || ||||| || || | || ||||| || || ||||| ||||||||||||||||| ||||| |
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
------------gtaagaaattttctttcttactcttgaaggctcgtgttc-ttgggtctaaacacttcttacttt------gtttcttt-------cagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
||||| |||| || | | || | | | | | | || || | | | | | ||| ||||||| |||||||||||||| || |||||||| ||||||||||| || ||||| || ||| | || |||| || || ||| | ||||||||||||||||| ||||| |
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 1
--------------gtaagaaattttctttcttactcttgaaggctcgtgt-tcttgggtctaaacacttcttactttgtttcttt-----------cagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
||| | | || || | | | | || | | | ||| || | | | | | ||| || ||| |||||||||||||| ||||||||||| ||||||||||| || ||||| || || | || |||| || || ||| | ||||||||||||||||| ||||| |
ttctctagtggcttgtatggatttggctctaatttcatgaagtgcacctatgcctttagtttcagtgcattacaatttattggttttttatggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
---------------------gtaagaaattttctt-----tcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
|| | || |||| | || | || | | | | | || || || | | ||| |||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| || || ||||| || || || ||||| || |||||||| ||||| |
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------gtaagaaattttctttcttactcttg----aaggctcgtgttcttggg------tctaaacacttct----tactttgtttcttt---cagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
| |||| | ||| | || || | | | ||| ||| | | ||| | | |||| | | ||| ||||||||||||| || || || ||||| || ||||| || ||||| || || | ||||| || ||||||||||||||||| ||||||||||| || ||||
gtaatgtttccttttttccaaatctcgactctgttttctgaattaaagttagggtttttgaaacgatctttggtttcttatgtggtgctttatctttttgtgtagGATATTGGAGGATGCGATATTCAGAAACAGGAAATTCGTGAGGCTGTTGAATTGCCTCTTACCCACCACGAGCTTTACAAACAGATTGGTATTGACCCAC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 1
---------gtaagaaattttctttct-------tactcttgaaggctcgtgttcttgg-----gtctaa-----acacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
|| | || || || | | | | || | | | | | ||| || | | | || || | || | | ||||||||||||| ||||| || |||||||| |||||||| || || || ||| | ||| |||| || || ||||| ||||| ||||||||||| ||||| |
tatttgaatgtttgccatctttttattgtaaacacatttctaaatggttggggttctggtcagagtttgaaattcatggtttttttgtaccttttattagGATATTGGAGGATGTGATATTCAGAAGCAGGAAATCCGTGAAGCTGTTGAGTTACCTTTGACTCATCATGAGCTGTACAAACAGATTGGTATAGATCCTC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------gtaagaaattttctttcttactcttgaaggctcgtgttcttg----ggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
| | | | ||| | | | | | |||| | | | | | || ||| | | ||||||||||| || |||||||| ||||||||||| || | || || || |||||||| || || ||||||||| | || |||||||||||||| || ||||
ttttgcgtagatttgtttggatgcacagttctattgttccagtattcgtacgttttcaatcttcagatgatttcatggtattgtatgttgctgggtgcagGATATTGGTGGGTGTGACATTCAGAAGCAAGAGATTAGGGAAGCAGTAGAGCTTCCACTTACTCACCACGAGTTATATAAGCAGATTGGTATTGACCCAC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------gtaagaaattttctttcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
| | | || | | ||| | | | | | | | | || || | ||| | | | | ||||||||||| || ||||| || || || ||||| || | ||||||||||||||||| || || || || || || |||||||||||||| ||||| ||||
agaaaaatgatttccgttatagggttacgaagcagatgtcttagtttaattgttcccatttatatgcattgttcaaagcgattcgtgttcg--tgagtgcagGATATTGGTGGATGTGATATACAAAAACAAGAGATTAGAGAGGCCGTGGAGCTTCCACTTACACATCATGAACTATACAAGCAGATTGGCATCGACCCAC
upper sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------gtaagaaattttctttcttactcttgaaggctc-gtgttcttgggtctaaacact-tcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
|| | || | ||| | |||| | | || || | | | | | || | || | | ||||||||||| || || || || ||||| ||||||||| | || || ||||||||||| || || || |||||| | || |||||||||||||| || ||||
aaggcttgttcatctgcatgaatctgtt-gttataatgtttgcaattcttacgagtgcagttttttaatactttcatattgtcgaatggtggtggatgcagGATATTGGTGGATGCGATATTCAGAAACAAGAAATCAGGGAAGCTGTGGAGCTTCCACTTACACATCACGAGTTATATAAGCAGATTGGTATTGACCCACMapped 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|169033191|gb|FE441211.1|FE441211EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST:
gi|169062255|gb|FE471069.1|FE471069EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST:
gi|169109987|gb|FE511135.1|FE511135EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST:
gi|169064808|gb|FE476128.1|FE476128EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST:
gi|169100216|gb|FE502937.1|FE502937EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST:
gi|169033190|gb|FE441210.1|FE441210EST: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
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),
34 (downstream exon)
Score:
31GCACCGCCATTCCAATGCGCTCGTCGACGTCCTTCCTCCAGAGGCGGATTCCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
ttcttac putative branch site (score: 31)
cacttcttactttgtt CT-rich tract
ttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaattttctttcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT