Sequence
atgc intronic sequence ATGC exonic sequence...gaaaacttcattggtaatggacattgcttcattggattttccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
Basic information
species | Glycine max |
transcript | GLYMA10G43230.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------------------------------gaaaacttcattg--gtaatggacattgcttcattggattttccttcttggaatttccactcaatc-taaatatgaatgattgttgcttgtcttat---catgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
| || | ||||| || | | || | | ||||||| || || | || | || | | || |||||| | | |||| ||||| || ||||||||||| || |||||||| ||||| || || ||||| ||| | |||||||| || |||||||| || ||||| || || ||
gtaggccttttagaaagattttttttttcacttgattctttgtgtgtacttttattctgagtagggttggttttaacactgtaatcatgatctatgc-cccctcttacttatttggaatcaagccttgttcatttatttttgtggtgaaagtttttcttatttgcttccagGCCATTGACGCAAGAGATGCTTTAGCAAAGTCAATCTATGCCTGCCTATTTGACTGGCTAGTTGAACAGATTAACAAATCTCTTGCGGTGGGAAAGAGGA
upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
-----gaaaacttcattggtaatggacattgcttcattggattt-tccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
|| | | | | | |||| | || | |||||||| | ||| | | || || | |||| | ||| | || | | |||| |||||||| ||||||||||| || || ||||| ||| | || |||||||| ||| |||||||||| || |||||||| || || || || || || |
agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaat----tttacattttcttgatatt--ctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC
upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
---------gaaaacttcattggtaatggacattgcttcattggattttccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
|| || |||| | | || |||| || | | |||| | | | | | ||| | | | ||| || | || | |||| ||||| | ||||||||||||||||| ||||| ||||||||| | ||||| ||| |||| |||||||| ||||| || || || || || ||| | |
gtctaatttttgaatttggagtaacttggataaaattccac-ggatatttgta--agacattttccccta---tgattattatcaaatcttgttt---tcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
atctaaa putative branch site (score: 3)
cttgtctt putative PPT
aatctaaatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaacttcattggtaatggacattgcttcattggattttccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC
- - -cttcatt
- - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - ccttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct