Sequence
atgc intronic sequence ATGC exonic sequenceGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgtactgatggtacgctttgtttcttgcagctgctaacactgtcaatcacag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ12300 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os01g27150.2 (Oryza sativa), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgt-actgatggtacgctttgtttcttgcagctgctaacactgtcaat-cacag------------------------------------------------
||| || ||||||||||| || || ||||| || || |||||||||||||||||||| || ||| | || | || ||||||||||||| |||||||| | | || | || | ||| || ||| | | | ||| | |
GACGATTTACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGAGAAGTACCGCGAGTCCTTCGAGGAGTACATCACGTCCATGgtgagcggctgttgggttcctccctt-cattgactagctcgattaatgcgctcctgtgttgaattttctaacgcagatgggttagggatagcgttgaaatt
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgtactgatggtacgctttgtttcttgcagctgctaacactgtcaatcacag----------------------------------------------------
||| || ||||||||||| || || ||||| || || |||||||||||||||||||| || ||| | || | || ||||||||||||| |||||||| || | ||| ||| ||||| | | | ||| |
GACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTACCGGGAGTCATTCGAGGAGTACATCACCTCCATGgt---gagacgatctttttttttctgcagttcttgtaaatgtttgatatgattgtgcatgtctgtcatttccggttggattcgatagtaggtgatttggggtt
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G166089_T01 (Zea mays), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgta------ctgatggtacgc-tttgtttcttgcagctgctaacactgtcaat-cacag-----------------------------------------
||| || ||||||||||| || || ||||| || || |||||||||||||||||||| || || | || | || |||||||| |||| |||||||| ||| | || | | | | || || | | | | || |
GACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTATCGGGAGTCGTTCGAGGAGTATATCACCTCCATGgtgagcctcctgttcatatctatctttcccatgtgaatgtctgtattagaacttcattgttttgtatttgcggcgttgtattaaggttagatttcctact
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G166089_T04 (Zea mays), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgta------ctgatggtacgctttgtttct-tgcagctgctaacactgtcaat-cacag-------------------------------
||| || ||||||||||| || || ||||| || || |||||||||||||||||||| || || | || | || |||||||| |||| |||||||| ||| | || | || | || || | | | | || |
GACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTATCGGGAGTCGTTCGAGGAGTATATCACCTCCATGgtgagcctcctgttcatatctatctttcccatgtgaatgtctgtattagaacttcattgttttgtatttgcggcgttgtattaaggttag
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G166694_T01 (Zea mays), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgt-actgatggtacgctttgtttcttgcagctgctaa-cactgtcaatcacag-----------------------------------------------
||| || ||||||||||| || || ||||| || ||||||||||| ||||||||||| || || | || | || |||||||||||| |||||||| | | | | |||||| || || | | ||
GACGATATACAACATGTGCACGCAGAAGCCGCCGCAGGACTACTCACAGCAGCTCTACGACAAGTATCGGGAGTCGTTCGAGGAGTACATCGCCTCCATGgtgagccgcttcatcatatccctcttgctcatgtgaatcgacctagattgtttttgtatctgcggcgtggtattaggatcaaatttcctacttcgagtgg
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: EDP03504 (Chlamydomonas reinhardtii), 5'ss of exon 3
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgta---ctgatggtacgctttgttt---cttgca--gctgctaacactgtcaatcacag-----------------------------------------
|||||||||||||||||| ||||| ||||| || || ||||| ||| ||||||| || ||||| || || || | ||||||| || | ||| || ||| | | | || | ||| || | | | | | | |||
GACTATCTACAACATGTGCACCCAGAAGCCGCCGCACGACTATTCGGAGCAGCTGTACAGCAAGTACAGGGACGCGTTCAACAAGTACATAAACGAGAAGgtgcgccttctggcgcaccccgcttgaacccgcattgcgcccacgcccatacagcccaggccacacacagcattgcagctttgtacgttgccacccgatc
upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S144_158V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgtactg--atggtacgctttgtttcttgcagctgctaacactgtcaatcacag-----------------------------------------------
|| || |||||||||||||| || |||||||| ||||| ||||| ||||| |||||||| ||||||| || | || || || |||||||| |||| ||| | | || || | ||| || | | | | | | |
AACCATATACAACATGTGTACGCAGAAGCCTCCTCAGGATTACTCTCAGCAACTCTATGACAGATACAGGGAGTCCTTCGAAGACTACATCAAATCCAAGgtgcagtcattgtgggattttatttatttatttatttatttatatattttttatttcccatgagagatgttactgaattcagtgagtttttggaacacggMapped 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|169024336|gb|FE436185.1|FE436185EST: GGAGTACATCAATTCCATG GTGATGCCCGCGCTCCGAGAGAAGCACAACGAGTTCATGCTCAGGGAGCTG
genomic: GGAGTACATCAATTCCATGgtactgatgg ... tcaatcacagGTGATGCCCGCGCTCCGAGAGAAGCACAACGAGTTCATGCTCAGGGAGCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATGgtactgatggtacgctttgtttcttgcagctgctaacactgtcaatcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG