Sequence
atgc intronic sequence ATGC exonic sequence...tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
Basic information
species | Glycine max |
transcript | GLYMA07G38050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4
tttttttactttggggtttatttgtct--aacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
|| ||| || | | ||| ||| ||| | ||| | | ||| | | | | | | | | | |||| | ||||| || |||| |||||||| ||||||||||| ||||| || || ||||||||||| ||||||||||||||||| ||||| || |||| ||||| |||
ttctttgtgattaaaatgagtccgtcacagactcgtgcaatctcatcagtttatgttaactactaaatgatc--attatattcttgttggtttacttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 4
-----------tttttttactttggggtttatttgtctaacttgtggattct-------ttgtattcgtat---ctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
| || || | | || ||| | | | | || || || | || ||| | | | | | ||||| | || || |||| || ||||||| | ||||||||| | || |||||||| |||||||| || ||||||||||| ||||| |||||||| || |||||||| |||| |||||||||
gtgagctcctttcccttcacaattatttgtaactgtatcataagagtatgctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatata--ttttttgctctgcagGTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtca--cttgaatgtgacatggcttgtttgt---tcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
|| | | ||||| | || | | | |||| | ||| | | | | ||||| | | | || || | || |||||||| |||||||||||||| ||||||||| | ||||| | ||||||||||| || | |||||||||||||||||||| ||||| || |||||||||
----cgtaaccatacatatttttgtg-acctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaa--tgtgacatggct--tgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
||| | | || | ||| | | || |||| ||| | ||| | | | | || | | ||| | | | || | ||||||| || |||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| ||||||||||| ||||| ||||||||||||
---gtttgatatattcttcagttg-cgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
tttttttactttggggtttatttgtctaacttgtggattcttt---gtattcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
|| | ||| ||| || | || | || | || | | | ||| | | | | | | ||| ||| ||||||| || || |||||||| ||||||||||||||||| ||||||||||||||||| |||||||||||||||| ||||| || || ||||||||||||
---ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
atctaat putative branch site (score: 3)
cttgttt putative PPT
tatctaatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatgtgacatggcttgtttgttcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - ggggttt
- - - - - - - - - - - - - - acttgtg
- - - - - - - - - - - - - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggct