Sequence
atgc intronic sequence ATGC exonic sequence...tttcctttaagtgttacaaaattaccagctcttctactcatgaatatatccccctgaaaggctgccctgattattgtcattaattatgttttcacctcagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
Basic information
species | Glycine max |
transcript | GLYMA13G20090.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 3'ss of exon 6
tttcctttaagtgttacaaaattaccagctcttctactcatgaatatatccccctgaaaggctgccctgattattgtcattaattatgttttcacct---cagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
||| | || | | | | | | | | | ||| | | | | || | | | |||| | | ||| | || |||| || |||||| || || ||||||||||| || |||||||| || || ||||| |||||||||||| | | || || ||| | |
--agttttcaatggcataga-taatgaattaaccaaaccattattgaactagcgtggacctttttaatcattactattattgagtaacttttggacttatcagGGACGAAGAGTTAGCAACTGAGGTGGCATGGGTTGTGGTCTATCTTTCAGCACTTTCAGACAGAGGTATTAGCTTAATA---------------------
upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165692_T01 (Zea mays), 3'ss of exon 6
tttcctttaagtgttacaaaattaccagctcttctactca-tgaatatatccccctgaaaggctgccctgattattgtcattaatta--tgtttt---cacctcagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
| | ||||| | || | || | ||| | | || | ||| ||| || ||| || | || | |||||| | | |||||||||| ||| | | |||||| || |||||||||||||| ||||| |||||||||||| | | |||||||||| | | || | || | | |
----ttctgcatgtta--atatcatcaaccaactaactaaatctatcgaatccctgtgcttgctttgctccttactgctgctgatgaattgttttggacccttcagGGATGAAGAACTTGTAACTGAGGTGGCATGGGTGGTTGTCTATCTTTCAGCACTTTCAGAAAAAGCTACCAGCCTAATAGTAAGAAGTTCGATGCCACAG
upper sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g02290.t01 (Vitis vinifera), 3'ss of exon 6
tttcctttaagtgttacaaa-attaccagctcttctactcatg-aatatatccccctgaaa-ggctgccctgattattgtcatta-attatgttttcacctcagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
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--cccagaaatttttgtttttattcgcaaaaattccactaatgtaaagttttatgttgaaacaacagagctaa--agtataattagattattggtcaaattcagGGATGAAGAGTTGGCAACTGAAGTAGCATGGGTGGTAGTTTATCTCTCAGCCCTTTCAGACACTGCCACTAGCATACTGGTGAAGAGTAATCTCCTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatccccctgaaaggctgccctgattattgtcattaattatgttttcacctcagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
cattaat putative branch site (score: 3)
ttttcacctc putative PPT
attattgtcattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcctttaagtgttacaaaattaccagctcttctactcatgaatatatccccctgaaaggctgccctgattattgtcattaattatgttttcacctcagGGATGATGAATTAGCAACTGAAGTAGCATGGGTGGTTGTTTATCTATCAGCACTTTCAAATATAGCTACCAGCATGCTGGTGAAGAGCAATGTACTCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - cttctac
- - - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgccct