Sequence
atgc intronic sequence ATGC exonic sequencegtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
Basic information
species | Glycine max |
transcript | GLYMA06G47420.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 11
gtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
||| | | | | || | || | || | | ||| | | | | || ||| || | || | ||| |||| ||||||||||||||| ||||||||||||| ||||| || ||||| ||||| || ||||| ||| | ||||| || || | ||| | | || |
-----------------gtaagaaacctagacctgattataaactgatggttaa----tcaattgaagacgttcctctcacctgtaaa----tcatgtattcttgcagATTGGCTGGATCTATGGTTCAATTACAGAAGATATCTTGACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCTATTTACTGCATTCCAAAGCGGCCAG
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 12
gtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaa--aaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG----------------------
| || || || ||||| || | | | || ||| || | | || | | || | | | | |||| |||| ||||||||||| ||||||||||||||||| | || ||||| || |||||||||||||| ||| | || || || || | |||| | | ||
-----------------------gtgaagtctagagcttgtggttattgct----ttatgagtca-aaacatatgttagatagtgaatcatatgtcatcttacttttcagattggctggatctatggatcagTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTGCATTCAAAGGTTCTGCACCTCT
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 12
gtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaa--aaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
| || || || ||||| || | | | || ||| || | | || | | || | | | | |||| |||| ||||||||||| ||||||||||||||||| | || ||||| || |||||||||||||| ||| | || || || || | |||| | | ||
-----------------------gtgaagtctagagcttgtggttattgct----ttatgagtca-aaacatatgttagatagtgaatcatatgtcatcttacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG
upper sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 12
gtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
| || | | || | | || | ||| ||| | | | | | || || | | || | || |||| |||| ||||||||||| ||||||||||| ||||| | || ||||| || |||||||||||||| ||| | || || || || | |||| | | ||||
----------------gtaaagtcttgagc----ctgtggttattggttgatgagtcaaaacatatgt-tacatagtgaatcatatgatattttcctt-----ttcagATTGGCTGGATCTATGGATCAGTTACAGAGGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
ttccttta CT-rich tract
tctaaaaaaattcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgaaatctttccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcagGTTGGGTGGATCTATGGTTCAGTTACAGAAGATATATTGACAGGTTTTAAAATGCATTGTCATGGATGGAGATCTATATATTGTACTCCTAGAAGACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC