Sequence
atgc intronic sequence ATGC exonic sequenceAAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcgattctaatgggtacgatgttgagcaaacccgtgtgtttccgcag
Basic information
species | Selaginella moellendorffii |
transcript | EFJ12094 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ12094 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G039089_T02 (Zea mays), 5'ss of exon 2
------AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCG---AGTgtgggattcgat---tctaatgggtacgatgttgagcaaacccgtgtgtttccgcag-----------------------------------------
| | || | |||| ||||| ||| | |||||| ||| ||||||||||||||||| ||||||||||| || || || ||||| |||| ||| | | | | | | | || || | | | | ||| | ||
AGGTCCAGAGACGATCGAGGACTTTGCTCAAATGCAATCGCAGGAGATTGAAGACAACATCATGAGCCGACGCAACAAAATTTTCCTTCTGATGGAAGAGgttttcagttttgaacactgtgtgtttcatttgtccagttctagctatctatttgtagctttgctaagacaccatggtgaagttttctgtatggaaaatttaatcag
upper sequence: EFJ12094 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA10G08680.1 (Glycine max), 5'ss of exon 2
------AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGT-
| | || || |||||||| ||| ||||||||||||||| |||||||| | |||| | ||||| || |||||||| |||||||| |||| || ||| | | ||| || || || ||| || || | | | || |
GGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATCTTTCTTCTCATGGAAGAGgttagctaattataataataatggcaccccattactctttagtgactatagcttttggaattgtgccaatttgcttatgtctttaactgatctgaatggtgtcgtgagattcatgtaaccgacttcacctagtgggataagactttcgttgttgttgtgaattgttattgtgttgagtatggcag
upper sequence: EFJ12094 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G36240.2 (Glycine max), 5'ss of exon 2
AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcgattctaatgg-gtacgatgtt-gagcaaacccgtgtgtttccgcag--------------------------------------
||| ||||||||||||||| |||||||| | |||| | ||||| || |||||||| |||||||| |||| || | || || || | |||| | | | |||| | |
-------------------------ATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATCTTTCTTCTCATGGAAGAGgttagcttataataatggcgtaccaatgttagttgtttgtttattttagaatgttagtgtgggattcgaacccacgacctctcctctcccttcttccttc
upper sequence: EFJ12094 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G36240.1 (Glycine max), 5'ss of exon 2
------AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcgattctaatgg-gtacgatgtt-gagcaaacccgtgtgtttccgcag--------------------------------------
| | || | ||||||||| ||| ||||||||||||||| |||||||| | |||| | ||||| || |||||||| |||||||| |||| || | || || || | |||| | | | |||| | |
GGGGCCAGAGACGATTGAGGATTTTGTGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATCTTTCTTCTCATGGAAGAGgttagcttataataatggcgtaccaatgttagttgtttgtttattttagaatgttagtgtgggattcgaacccacgacctctcctctcccttcttccttc
upper sequence: EFJ12094 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S380_25V6.1 (Physcomitrella patens), 5'ss of exon 2
------AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcgattctaatg------------ggtacgatgttgagca--aacccgtgtgtttccgcag--------------------------
|||||| || | || ||| | ||| ||||||| ||||||||||||||||| | ||||| ||||| ||||| || || |||||||| |||| | || |||| | || | | ||| || |||| | || || |
AGGACGAAACACTGTTCTTGACTTTTCCAAAATGCAGCTGCAAGAAATTCGTGACAACATTACAAGCCGTCGCAATAAAATATTCCTTCTCATGGAAGAGgtataaactgcatctacttctggtactgcttttccaccgttctctaatgaccagcaaccaggccccttacgttgcctgccaggtgattgcatttttgcgcMapped 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|169075975|gb|FE480983.1|FE480983EST: ACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCAT---GGA-G-GAG- GTGAGAAGGCTGCGGATCCAGCTGCGAATCAAGAACGCAGAGCAAGGAGTG
genomic: ACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcg ... gtttccgcagGTGAGAAGGCTGCGGATCCAGCTGCGAATCAAGAACGCAGAGCAAGGAGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAACACAGTGCAGGATTTTGCAGCCATGGAGCTGCAGGAAATTCGTGACAACATCATGAGCCGCCGCAACAAAATCTTTCTGCTCATGGAGGAGGCGAGTgtgggattcgattctaatgggtacgatgttgagcaaacccgtgtgtttccgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG