Sequence
atgc intronic sequence ATGC exonic sequencegtgattatttggggttggagctgtttttccttcatgtgtattcagtttattctttctaactaactacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG
Basic information
species | Glycine max |
transcript | GLYMA18G45120.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------gtg-attatttggggttggagctgtttttccttcatgtg----tattcagt---ttattctttctaacta--actacttttgt--acagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------
|| | ||| || | | | | ||| | ||||| | | |||| | ||||||| | || | | ||| | ||||| | || || || | |||| | || | |||| | ||||||| || |||||||| ||||| ||||||||||||||||
gtataaaagtactcttttctatagtttgctatcatcttgtatagtatgaggcactaatgtt-tctttacaacatgttgatctgtccagtatctaattctttttgtcttttgtcattcctgtttatagTTGCTCCTGAATGGTGCAAGTGCGAATGGAGCGAAAAAAATCCGTGTTCACATTCTTACTGATGGACGTGATGTTTTGGATGGCACAAGCGTTGGTTTTG
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------gtgattatttggggttggagctgtttttccttcatgtgtattcagtttattctttctaacta--actacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------
|| | | || | | || | || | ||| | | | |||| || | | | |||||| ||||||||| |||||||| | ||| || |||| ||| ||| || | |||||||||||||| ||||| ||||||||||||||||
gttttgatttgatatgttcttcattattttgttcaaattctggttta-atgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgattatttggggttggagctgtttttccttcatg----tgtattcagtttattctttctaactaactactttt--gtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------
|| ||| || | | |||| || || | ||| ||| | | ||| | | || || || |||||| ||||||| || || || || |||| ||| ||| |||| |||||||||||||| ||||| ||||||||||||||||
gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtgattat-ttggggttggagctgttttt----ccttcatgtgtattcagtttattctttctaactaactacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------
|||| ||| | ||||| | |||| || | | ||| | || || | | || | || ||| ||||| | | ||||||| ||||||| |||| |||||| ||||||||||||| ||||| ||||| ||||||||||||||||
gtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggagatca--tgatcctctttggctt-tttctcttg-gcagTTACTTTTAAAAGGAGCTAGTGAGAATGGTGCAAAAAGAATCCGTGTCCATATCCTTACTGATGGGCGTGATGTTTTGGATGGTTCCAGTGTTGGGTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttccttcatgtgtattcagtttattctttctaactaactacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG
aactaac putative branch site (score: 1)
ctactttt CT-rich tract
tttattctttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattatttggggttggagctgtttttccttcatgtgtattcagtttattctttctaactaactacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG