Sequence
atgc intronic sequence ATGC exonic sequencegtaagctctacttcttcctgttatcacttacagaccagctttccccttctcttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ28891 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28891 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA20G30860.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gtaagct--ctacttcttcctgttatcacttacagaccagctttccccttct--cttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
||| ||| ||||| || || | || || | | || ||| |||||||||||||||||| |||||||||||| | || || ||||| | ||||| ||||||||||| | | | | | ||||||||| |||||||
gtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgtt-ctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
upper sequence: EFJ28891 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G08790.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------gtaagctctacttcttcctgttatcacttacagaccagctttccccttctc----ttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
| | | | | || | | ||| | | || ||| || ||||||||||||||||||| ||||||| |||| || || |||||||| | | || ||||||||||| | || | | | ||||||||| |||||||
gtacgatagtttgcattgaccatgttcttgatgttatgataactgctttttcaattgatgttcctggcttgtttacgtgtttcttgtaatttatttatttgtttatggcttttccaatttgcagAGGAACTACCGTTACTTCTTTCTGTTTGTTTCTTCGGCAACTATTCTATGTATCTATGTGTTTTCCATCTCAGCTTTTTACATCAAGGTTCTGATGGATC
upper sequence: EFJ28891 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA16G27910.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------gtaagctctacttcttcctgttatc-acttacagaccagctttccccttctcttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
| |||| | ||| ||| || | ||| ||||||||||||||||||| ||||||| |||| || || |||||||| | | || ||||||||||| | || | | | ||||||||| |||||||
gtatgatagttggcattgaccatgttcttgatgttatgataactgctttgttcgattgatgttcctggcttgctcacgtgtttcttgtaatttatttatttgtttatggcttttccaatttgcagAGGAACTACCGTTACTTCTTTCTGTTTGTTTCTTCGGCAACTATTCTATGTATCTATGTGTTTTCCATCTCAGCTTTTTACATCAAGGTTCTGATGGATC
upper sequence: EFJ28891 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S36_22V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------------------------gtaagctctacttcttcctgttatcacttacagaccagctttccccttctcttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
|||||| | | || | || | | | | | ||||||||||| || || |||||||||||||||||||| || | | || ||||| || ||||| ||||| |||||| | | ||||| || | |||||||||
gtacgcacttttcttgttctatcacctatactacttaggcacattcgatgaattatgatgcgttggtgtgttattgatcatactttgttggttatacgagtttggttgatggtattgctgtaagagctctcacacgcctgattgtttctcgtggtcaattgtactgtgatgtttgcagAGGAATTATCGATTCTTCTTTATGTTCGTGTCATCAACTTCACTTTTGTGTGTGTATGTCTTTGCAATGTGCGCATTGTACATAAAAATCTTGATGGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagctctacttcttcctgttatcacttacagaccagctttccccttctcttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
cacttac putative branch site (score: 2)
ccagctttccccttct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctctacttcttcctgttatcacttacagaccagctttccccttctcttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA