Sequence
atgc intronic sequence ATGC exonic sequencegtattttaaacgcagggcttacaatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31227 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 11
---------------------------gta-ttttaaacgcagggcttacaatgtctta------ctcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
|| |||||| | || | || | || || |||| ||||||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| || || || || ||||| | |||||||| ||| ||| || ||||| |||
gtatgtgtaataccatttggataatgtgtgcttttaagcatttatgttctattgccctaagatatctttctcttattgtttcagGGTGAGTATTCATGAGGCCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCA
upper sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
---------------------------------gtattttaaacgcagggcttac----aatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
| |||||| | |||| ||||| | || | ||| ||||||||||||||| |||||||| |||||||| || |||||||| || |||||||| || || || ||||| | |||||| | ||| ||| || ||||| |||
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctg-attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
upper sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------gtattttaaacgcagggcttacaatgtcttactcgggagtattttt----tcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
| | | | || || | | | ||||||| |||||| ||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || || ||||| | || || || |||||||| || ||||| |||
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA
upper sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
---------------------------------------gtattttaaacgcagggcttacaatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
|| ||| | | | | | | || | | | || |||||| || || |||||||||||||||||||| ||||| ||||| ||||||||||| || || ||||| | || || || || ||||| || ||||| |||
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttaaacgcagggcttacaatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
gtcttac putative branch site (score: 3)
tattttttc putative PPT
tattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttaaacgcagggcttacaatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT