Sequence
atgc intronic sequence ATGC exonic sequencegtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
Basic information
species | Glycine max |
transcript | GLYMA03G40220.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatct-gatccattgtttttg----cctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
| | || | || | ||| || | | | | ||| || |||| ||||| | | | ||||| | ||| ||| ||||| | ||||| || ||||| || || ||||||||||||||||||| || ||||||||| ||||| |||||||| | | | | |||| |||| ||||
-----------------------------------------------------------------ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 12
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
|| | ||| | ||| || | ||||| | ||| || | ||| | | || || | | ||||||| | || | || || ||| || | ||| ||| ||||| |||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| || | | | || |||||| ||||| |
-----------------------acactaaat--tccatgtttat-agctt---gaatgttagctcacaaaataaatcaat-------cttattcatgtagtggg-------taatataat------ttcttgactga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 11
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
|| | ||| | ||| || | ||||| | ||| || | ||| | | || || | | | | ||||||| | || || | | | ||| | ||| ||| ||||| |||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| || | | | || |||||| ||||| |
------------------------cactaaat--tccatgtttat-agctt---gaatgttagctcacaaaataaatcaa--tctttattgat----gtagtggg--taatataattt---------------cttgattga------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 8
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
||| | |||| || | || ||| ||| || | ||| | | || || | | | | ||||||| | || | || || ||| || | ||| ||| ||||| |||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| || | | | || |||||| ||||| |
--------------------------gtgagaggcttatg---ctaatagcttgaat-gttagctcacaaaataaatcaa--tctttattgat----gtagtggg-------taatataat------ttcttgactga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAAATGATGGTACCGTATCAC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00540.t01 (Vitis vinifera), 3'ss of exon 9
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
|| | ||| | ||| || | ||||| | ||| || | ||| | | || || | | | | ||||||| | || | || || ||| || | ||| ||| ||||| |||||||||||||||| || || || |||||||||||||||| || |||||||| ||||| ||||| || | | | || |||||| |||| |
------------------------cactaaat--tccatgtttat-agctt---gaatgttagctcacaaaataaatcaa--tctttattgat----gtagtggg-------taatataat------ttcttgactga----------attccttt-cagGCTATAATGGAGGTTGGAGAGGTAATACAATTTTATGATTCTGATAAGCGCTTTCCTGCATGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC
upper sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 9
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
|| | ||| | ||| || | ||||| | ||| || | ||| | | | ||| | | | | ||||||| | || || | | | ||| | ||| ||| ||||| |||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| || | | | || |||||| ||||| |
------------------------cactaaat--tccatgtttat-agctt---gaatgttagctcacaaaataaatca--gtctttattgat----gtagtggg--taatataattt---------------cttgattga------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
aattaac putative branch site (score: 2)
tttattt putative PPT
taattaacacaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatctgatccattgtttttgcctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG