Sequence
atgc intronic sequence ATGC exonic sequencegtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ18599 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
|| | | | ||||| | ||| | | | | | | | | | ||| || || ||||| || ||||||||||||||||| || || |||||||| || |||||||| || ||||||| || ||||| ||||| || |||
gtccggctctctcttttttttttacatatttttactgttatatctcagcttagcctgagcttgttttatccatatcaattcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
| | | ||| | | || ||| || | | | ||| || ||| || || |||||||| || ||||| || || ||||| || |||||||||||||| ||| || || ||||||||||||||||| ||||| ||||||
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g37890.3 (Oryza sativa), 3'ss of exon 2
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG------
| | | ||| | | || ||| || | | | ||| || ||| || || |||||||| || ||||| || || ||||| || |||||||||||||| ||| || || ||||||||||||||||| ||||| ||||||
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGGTTTCT
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gtagcctg--tgatgtttctaagttgttcttcccaaggatt-------tggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
||| || ||||| | | || || ||| || || | | | || || | | || ||| || || ||||| || ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||| || ||||| ||||| || |||
gtatatatacaaatatattgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg-------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
|| | | || | | || || | | || | | ||| |||| || || ||||||||||| || ||||| || || || || || || |||||| ||||||| || ||||||||||||||||| ||||| ||||| || |||
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
-----------------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttgg--------cttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
| | | ||| | | | | || || || | | | | || |||||| ||||||||||| || ||||| || || ||||| || ||||| ||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------gtagcctgtgatgtttctaagtt---gttcttcccaaggatttgga--gctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
|| || | | || | || ||| | || | || | | | | ||| || |||| || || |||||||| || ||||| || || || || |||||||||||| ||||||||| | ||||| ||||||||||||||||| ||||| ||||||
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt-agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------------gtagcctgtgatgtttctaa---gttgttct--tcccaaggatttg--gagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
| || | || | || |||| || |||| ||| || ||| | || | || | | ||| || || ||||| || ||||| ||||| ||||| || ||||||||| |||| ||||| ||||| ||||||||||| ||||||||||| ||||||
gtttgttgtcttcaatttgttctatcctggctttgactaagttctccatttgatatgaaaattggtttcatgtactcagcatttatctgtctaggagac-gtaaatttactaatgaatttttctggtcctgagaattctctaatatctgattattccacattgtgcagGTTCTTCTATGCCTCTAGTGCTTGCATCTACCCTGAATTTAAGCAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCATGGCCTGCAGAGMapped 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|169064800|gb|FE476120.1|FE476120EST: ATGATCAGTTTCAACATGCTCGAGGCCTCCCGGATCAACGGAGTCAAAAG ANNNNNNNATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGA
genomic: ATGATCAGTTTCAACATGCTCGAGGCCTCCCGGATCAACGGAGTCAAAAGgtagcctgtg ... tggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGA
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:
22 (upstream exon),
35 (downstream exon)
Score:
4GAATGGGATTCATCCAGTCCAATCACTCTGTGATTCTCTTCAACAACACCATGATCAGTTTCAACATGCTCGAGGCCTCCCGGATCAACGGAGTCAAAAGgtagcctgtg ... tggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
agctcac putative branch site (score: 4)
ctcactctctttcttg CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG