Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttcttcgcatttgatttttttttcagAGCTTTTGGTTGATCTTGTTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ05569 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 1
-----------------------------gtgagtttcttcgcatttgattttttt------ttcagAGCTTTTGGTTGATCTTGTTGGTGGC-AATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------
||| ||| || | ||||||| | | | || | || | | | | |||||||||||| |||||||| ||| | || || ||||||||||| |||||||| || || || || ||
gtgcttatgaactgcctgaagattgcaacatga-tttatttgggggtgattttgtgggtgaacttgcgacattggaatgccttgacttgcgtttggcgtagAGGAGTTTGTGGCGCATTCATCCAATGTCAACTGCCTCAAGATTGGGAGGAAGACTTCACGAGTTCTCGTGACAGGAGGAGATGACCATAAGGTTAATCT
upper sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
-----------------------------gtgagtttcttcgc---atttgatt-tttttttcagAGCTTTTGGTTGATCTTG--TTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------
| ||| | ||| | | || ||| | |||| |||| ||| | |||||||||||| ||||| || ||| | || || ||||||||||| |||||||| || |||||||| ||
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattggaatgccttgacttgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT
upper sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
------------------------------gtgagtttcttcg---catttgatttttttttcagAGCTTTTGGTTGATCTTG--TTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------
|| |||| | ||| | | | | | ||| |||| ||| | |||||||||||| |||||| | ||| | ||||| ||||||||||| |||||||| || || ||||| ||
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagtttcttcgcatttgatttttttttcagAGCTTTTGGTTGATCTTGTTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT
atttgat putative branch site (score: 5)
tttgatttttttttc CT-rich tract
atttgatttttttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttcttcgcatttgatttttttttcagAGCTTTTGGTTGATCTTGTTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA