Sequence
atgc intronic sequence ATGC exonic sequence...tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
Basic information
species | Glycine max |
transcript | GLYMA17G02640.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4
--tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
||| | | | || | | | ||| ||| | ||| | | ||| | | | | | | ||| | ||| | |||||||| |||| |||||||| ||||||||||| ||||| || || ||||||||||| ||||||||||||||||| ||||| || |||| ||||| |||
ttctttgtgattaaaatgagtccgtcacagactcgtgcaatctcatcagtttatgttaactactaaatgatc--attatattcttgttggtttacttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 4
-----tttttttactttggggattatttgt--ctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatttgacattgct--------------tgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
| ||| | || ||||||||| || | | | | || |||| | | | |||||| | |||| | | || | || |||| || | ||||||||| | || |||||||| |||||||| || ||||||||||| ||||| |||||||| || |||||||| |||| |||||||||
gtgagctcctttcccttcacaattatttgtaactgtatcataagagtatgctgccaccattc--tgttaatataagttgaataataaattgttaaaatgtaatatattttttgctctgcagGTATAAAGGGGAAGATGCGAGACTACCAACTAGCTGGGCTTAATTGGCTCATACGGTTGTACGAGAATGGTATCAATGGTATATTGGCTGATGAAATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 4
tttttttactttggggattatttgtctaacttgtggattctttgtat-tcgtatctaatgttt-ttgtcacttg-aatttgacattgcttgttcg---ttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
| ||| | | | | || | | || ||| | |||| |||| ||| || || || ||| |||| | | |||||||| | || |||||| | ||||| ||| | ||||| || || ||||| |||||||||||||||||||| || ||||| || | || ||||| |||
------tctcatggaaaccaatcaataaggttttagttttcttgggccttgtattctttgttcattgctttatgtaaatttttattaaatgtttgaatctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 1
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtt---tttgtcacttg-aatttgacattgcttgttcg---ttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
| | || || | | || | ||||| | || |||| |||| |||||| || || | ||| |||| | ||| |||||||| | || |||||| | |||||||| | ||||| || || ||||| |||||||||||||||||||| || ||||| || | || ||||| |||
------gaaaccaaccaataatt-tttggttttagttttcttaggttttatatcctttgttccttttgtcttatgtaaacttttattaaatgtttgaatttctccagGCATCAAGGGAAAGATGCGTGATTACCAGTTGGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtca--cttgaatttgacat---tgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
| || | ||| ||||| | || | | | |||| | ||| | | | | ||||| || | | | | || || ||||| || |||||||||||||| ||||||||| | ||||| | ||||||||||| || | |||||||||||||||||||| ||||| || |||||||||
---cgtaaccatacatatt-tttgtg-acctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 4
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaa--tttgacattgct--tgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
||| | | | | ||| | | || |||| ||| | ||| | | | | || | | ||| || | | ||| | |||| || || |||||| | || ||||||||| | ||||| ||||||||||||| || |||||||||| ||||||||||| ||||| ||||||||||||
---gtttgatatattcttcagttg-cgagctcacaatttctaggtaggactgcataaattctgtagaatttagagatctgatcttcatactcttcatattgcagGTATTCAGGGGAAGTTAAGAGATTACCAATTAGCTGGTTTAAACTGGCTCATTCGGCTGTATGAGAACGGCATAAATGGGATTCTTGCAGATGAAATG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
tttttttactttggggattatttgtctaacttgtggattcttt---gtattcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
|| | ||| | | || | || | || | || | | | ||| | | | | | || ||| |||| || || || |||||||| ||||||||||||||||| ||||||||||||||||| |||||||||||||||| ||||| || || ||||||||||||
---ttagatcttgctgttgtttaagatgcattacagtttttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
cttgttc CT-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtcacttgaatttgacattgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - -tttgggg
- - - - - - - - - - - - - - acttgtg
- - - - - - - - - - - - - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt