Sequence
atgc intronic sequence ATGC exonic sequencegtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ25378 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ25378 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g12070.1 (Oryza sativa), 3'ss of exon 1
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctc---tcttagttttccttct-caaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
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------------------------------------------------------------gtacgtggagtcgttcaccattttctc-cgttcttgaattgcaggatgtgttctacagctccatgcatctgatctgttgattttttttcttt-tttcagGTGGATCTTGTTGGTGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGGCTGCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCATCGAGT
upper sequence: EFJ25378 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G453565_T01 (Zea mays), 3'ss of exon 1
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
|| | || | | ||| | | | || | | | | ||| ||| | || | | | || | | | | | || ||||||| ||||| ||| || |||||||| |||||||||||||||||||| || || || ||||| |||||| |||| ||| | || |||||||| ||||||
-------------------------------------------------gtctcagctgtatatttcataca-tggataactaataaaaaccggcatttattttgtttccttca---tcaatcaatcaataaatcaaatgtggtcc--actccagGTGGATCTGGTGGGCGGCTACTACGACGCCGGCGACAACGTCAAGTTCGGCCTGCCGATGGCGTTCACGGTCACCATGATGTCCTGGAGCGTCATCGAGT
upper sequence: EFJ25378 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
| | || | | | ||| | | || | || | || | || | ||| |||| | | || | | ||| ||| | || ||||| ||||| || ||| ||||| |||||||| || ||||||||||| ||||| || || |||||||| |||||| | || ||| | |||||| || | | ||||
-----------------gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttt-----tggttcttttatgttttgtctcgccgga-------cagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
upper sequence: EFJ25378 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S37_355V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
| | | | | || | | | | ||| ||| | | | || ||| | || | | | | || | | | | | ||| | || | || | ||||||| || |||||||||||||||||||| || ||||| ||||||| ||| || || ||||| || || || || |||||||| ||||| || | || |
------------------------------gtaagtggcacattccttgaactcacaacagtttctcgtgttgcgttgcagtacc--gcaatgtcgcagaataatgtgtcgtgatagctcacactgtat---ctgtgtggcgttgttccgtgtagGTTGACCTTTCGGGAGGTTACTACGATGCAGGAGACAATGTCAAGTATGGTCTGCCGATGGCGTTTACCATTACTATGCTCTCTTGGAGTGTAATTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
cactgac putative branch site (score: 2)
tctttgttcc putative PPT
aatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG