Sequence
atgc intronic sequence ATGC exonic sequence...atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
Basic information
species | Glycine max |
transcript | GLYMA03G40210.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
atgtatccttttacttcattatgttactgactaaa--ttcaataacggggtggcattg-tctgatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
| | | ||| | | | | | | |||| | || | | | ||| ||| | || | | ||| | ||| | | ||||||| ||||| || ||||| || || ||||||||||||||||||| || ||||||||| ||||| |||||||||| | | | | |||| |||| ||||
---ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 12
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
| || | | || || || | | || || | || | || | ||| | | | || | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||||||||| |||| || | || |||||| ||||| |
acactaaattccatgtttatagcttgaatgttagctcacaaaataaatcaatcttattc-atgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 11
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
|| | | || || || | | || || |||| | || | ||| | | | || | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||||||||| |||| || | || |||||| ||||| |
-cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaatataatttcttgattgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 8
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
|| | ||| | || || || | | || || |||| | || | ||| | | | || | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||||||||| |||| || | || |||||| ||||| |
gtg-agaggcttatgctaatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAAATGATGGTACCGTATCAC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00500.t01 (Vitis vinifera), 3'ss of exon 11
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
|| | | | || || | | || || |||| | || | ||| | | | || | |||||||||||||||| ||||| || || || ||||||||| ||||||||| |||||||| ||||||||||| |||| || | || |||||| |||| |
-cactaaattccatgtttacagcttgaaagttagctcacaaaataaatcaatctttattgatgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTCGGAGAGGTAATACAATTTTATGATACTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00540.t01 (Vitis vinifera), 3'ss of exon 9
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
|| | | || || || | | || || |||| | || | ||| | | | || | |||||||||||||||||||||| || || || |||||||||||||||| || |||||||| ||||||||||| |||| || | || |||||| |||| |
-cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTTGGAGAGGTAATACAATTTTATGATTCTGATAAGCGCTTTCCTGCATGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC
upper sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 9
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagt-atttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
|| | | || || || | | || | || |||| | || | ||| | | | || | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||||||||| |||| || | || |||||| ||||| |
-cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcagtctttattgatgtagtgggtaatataatttcttgattgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggtggcattgtctgatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
gcctaac putative branch site (score: 2)
tttatct putative PPT
agtatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtatccttttacttcattatgttactgactaaattcaataacggggtggcattgtctgatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - -cttcatt
- - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - - - -gggtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacac