Sequence
atgc intronic sequence ATGC exonic sequencegtaggggtattgtgttcttgcgcattttccccgtctctgatcgctggggttcttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ26984 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ26697 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------gtaggggtattgtgttcttgcgcatttt-ccccgtctctgatcgctggggttcttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
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gtcagtaaaacccgctccaaatctccatttgtttttccttcttctttttccgagggaggagattgttaatgtgatttgggttttgacattttttttttgggtt---agGTCGGACGGGGCGCAGCCGCACTTGGTGAACATTCAGTTCCAGAAGAAGGTGCAGCTGCAG---------------------------------------
upper sequence: EFJ26697 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 1
---------------------------gtaggggtattgtgttcttgcgcatt---ttccccgtctctgatcgctggggtt----cttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
|| | || | || | | | | || | || ||| | || | || || ||||| ||||||||||| |||||||||||||||||||||||||||||| |||||
gtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtc-ctgcgatttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG---------------------------------------
upper sequence: EFJ26697 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G174971_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------gtaggggtattgtgttcttgcgcattttccccgtctctgatcgctggggttcttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
|| | | | || | | |||| || | | ||| || || ||||| ||| ||||||| |||||||||||| ||||||||||||||||| |||||
gtcgtttaaatcgtagtttaatatcactcctttctttgtcgaattagttgaagctagaaggtcagagttggtgatttgggttctg--cgattttggtctcagGTCTGATGGGGCGGAGCCGCACCTGGTGAACATCCGGTTCCAGAAGAAGGTGCAGCTGCAG--------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggggtattgtgttcttgcgcattttccccgtctctgatcgctggggttcttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
ctctgat putative branch site (score: 4)
ttctt putative PPT
atttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggggtattgtgttcttgcgcattttccccgtctctgatcgctggggttcttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA