Sequence
atgc intronic sequence ATGC exonic sequencegtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ29127 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
------------------------gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
| | | | | || ||| | || | | |||||||| ||||| ||||| || || || ||||||||||| ||||| ||||| || |||||||||| ||| || || |||||||| || || ||||| |
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
--------gtaactatacttttgtgctgttag---------ctcgtttcttaccatgggt------ttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
|||| | | || | || || | | |||| || | |||||||| ||||| ||||| || || ||||||||||| |||||||| || ||||| || ||||| | | || || |||||||| || || ||||| |
gtgagtatgtaaagtgattctttgggtgataaatttaagaatttaatctaaaccagaagtactctgtgcagCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
-------------------------gtaactatacttttgtgct--gttagc-tcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
| | | ||| || ||| | ||| | || || | | |||||| | ||||| ||||| || || || |||||||| |||||||| || |||||||||||||||| || || || || ||||| || || ||||| |
gtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
-------------------------------------------------gtaactatacttttgtgct--gttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
| | | ||| || ||| | ||| || || | | |||||| | ||||| ||||| || || || |||||||| |||||||| || ||||||||||||||| || || || || ||||| || || ||||| |
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 9
---------------------------------gtaa--ctatacttttgtgctgttagctcgtttcttac-catgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
||| || | | || || || || | | | |||||||| || || || ||||| || || || |||||||| ||||| ||||||||||| ||||||||| || || ||||||||||| | || || || |
gtgaactaatcagtggagcttaatttcaatttcataagcctgttcactttaagcattggccacctttaaatacttaaatttcagCTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
-------------------------------gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
|| ||| |||| || | || | ||| | || ||||||||| ||||| || || || || | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| |
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 13
-------------------------------gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
||| ||| |||| || | || || ||| | || ||||||||| ||||| || || || || | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| |
gttggatatcactagtaaaaaataaatcctcataattattgttttacaatggtttgtcacttattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
upper sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------------------------------------------gtaactatacttttgtgctgttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
| | | | | || | | || || || || | | |||||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGMapped 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|169035471|gb|FE442862.1|FE442862EST: AGCTCATTGGTCTTGTTACGTCGAGGGATGAGATACCAGATCTTCTCAAG CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTT
genomic: AGCTCATTGGTCTTGTTACGTCGAGGGATGAGATACCAGATCTTCTCAAGgtaactatac ... tgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTT
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),
29 (downstream exon)
Score:
11GTGATTACGGAGGCGCTGCCAAAGTCTGTGGGAAAAGAGCTCATTGGTCTTGTTACGTCGAGGGATGAGATACCAGATCTTCTCAAGgtaactatac ... tgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
ttcttac putative branch site (score: 11)
tatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG