Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatcgatttagctttctagcagtgatgttttttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ28961 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28961 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os05g25850.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gtaaaatcgatttagctttctagcagtgatgttttttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAG---GCAAATTTGTAG-------
| || | | | | ||| || |||| | | || |||||||| ||||||| ||| |||||||| | ||||||||||| ||||| ||||||| ||| ||||| || | | |
gtttaacaacttacaacatcgtgcacacccaacttatttgtgcttcgaatttcaacctttgctattg-ctaaacagtctt-cattgatttccgtggttgcagTACAAGAATGTCAGGCCAGACTACCTGAGCAACATCTGGAAGGTGATGAACTGGAAATACGCAGGGGAGGTGTACGAAAATGCGACTGCTTGATGTTGTC
upper sequence: EFJ28961 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G124455_T02 (Zea mays), 3'ss of exon 5
------------------------------------------------------gtaaaatcgatttagctttctagcagtgatgttttttt--tttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG-----------
| ||| || | | || ||| || || |||||||| ||||| | |||||| ||||| || ||||||||||| ||||| ||||||| | | | ||||| | || |
atttgtctcccaatatcagtgtcagttttgtcgtgagtcaatcttgaagtgacctttttgtcgtgctaagtggtctcctccactgctttcttggttgcagTACAAGAATGTTAGGCCGGATTACCTGAACAACATCTGGAAGGTGATGAACTGGAAATATGCTGGAGAGGTGTACGAAA-ATGTTCTTGCTTGAATTGTCT
upper sequence: EFJ28961 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G032676_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------gtaaaatcgatttagctttctagc--agtgat----gttttttt--tttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG-----------
| || || || | | || || |||||| | ||| || || |||||||| ||||| | |||||| ||||| || ||||||||||| ||||| ||||||| | | | ||||| | || |
aatttatttgccctcccaatatcagtgttagttttgtcgtgagtaaatcttgaagagactttgttgtcgtgctaagtgatcactgctttcttggttgcagTACAAGAATGTTAGGCCGGATTACCTGAACAACATCTGGAAGGTGATGAACTGGAAATATGCTGGAGAGGTGTACGAAA-ATGTTCTTGCTTGAATTGTCT
upper sequence: EFJ28961 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G059991_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------gtaaaatcgatttagctttctagc--agtgat----gttttttt--tttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG-----------
| || || || | | || || |||| | | ||| || || |||||||| ||||| | |||||| ||||| || ||||||||||| ||||| ||||||| | | | ||||| | || |
aatttatttgccctcccaatatcagtgtcaattttgtcgtgagtcaatcttgaagagactttgttgtcgtgctaagtgctcactgctttcttggttgcagTACAAGAATGTTAGGCCGGATTACCTGAACAACATCTGGAAGGTGATGAACTGGAAATATGCTGGAGAGGTGTACGAAA-ATGTTCTTGCTTGAATTGTCTMapped 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|169046374|gb|FE454700.1|FE454700EST: TGGGAATTGATGTGTGGGAGCACGCTTATTATCTCCAG---T--AC--A- -A-AAA--TGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAAC
genomic: TGGGAATTGATGTGTGGGAGCACGCTTATTATCTCCAGGCATGGACTGATgtaaaatcga ... tttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAAC
EST:
gi|169050436|gb|FE458854.1|FE458854EST: TGGGAATTGATGTGTGGGAGCACGCTTATTATCTCCAG---T--AC--A- -A-AAA--TGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAAC
genomic: TGGGAATTGATGTGTGGGAGCACGCTTATTATCTCCAGGCATGGACTGATgtaaaatcga ... tttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaaatcgatttagctttctagcagtgatgttttttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG
tgttttttttttc CT-rich tract
tgatgtttttttttt 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
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gtaaaatcgatttagctttctagcagtgatgttttttttttcagTACAAAAATGTCAAGCCGGACTACCTCAAGAACATCTGGAAAGTGATCAACTGGAGCGACGTTTCTAGCAGATACGAGGCAAATTTGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT