Sequence
atgc intronic sequence ATGC exonic sequence...actttttattattccttatttatgtagtattcatatcatgtgagtttgtatttatttgatttgatgttgagttgctaactaactacacttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
Basic information
species | Glycine max |
transcript | GLYMA09G25590.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G25590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
actttttattattccttatttatgtagtattcatatcatgtgagtttgtatttatttgatttgatgttgagttgctaactaactac---acttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
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---------------gtctctctttcatcttcttctt-tattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttgatagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
upper sequence: GLYMA09G25590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------actttttattattccttatttatgtagtattc--atatcatgtg---agtttgtatttatttgatttgatgttgagttgctaactaactacacttaaatat----ctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
| || ||||| | | ||| | | || | ||||| | | | || || | ||| |||| | | | |||||| ||| | | | ||| |||||||| |||||||| ||||||||| ||||||||||||| ||| | || |||||| | ||||| ||| ||| || || | || |||| || ||
gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
upper sequence: GLYMA09G25590.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 1
actttttattattccttatttatgtagtattcatatcatgtgagtttgtatttatttgat-ttgatgttgagttgctaactaactacacttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
| || | ||| | | ||| || | | |||| ||| ||| | || | | || || | | | | || | ||| |||||||| ||||| |||||||||||| ||||||||||||||||||| || |||||||| || | ||| |||| | | | ||| |||| || ||
atgttcttttagtgcc-attgttgcatgttacataccatatgatcacatgttggtctagcattaatatgccttgattctttgaccttgtggtgcattgcagGTTTGCAAAGGAATGGAAAGAGCTGCAGATTAAGGTGGATTAACTACTTAAGACCAGGATTAAAACGCGGGATGTTTACGATCGAGGAGGAAGAGACGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatttatttgatttgatgttgagttgctaactaactacacttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
aactaac putative branch site (score: 1)
tttatttgatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actttttattattccttatttatgtagtattcatatcatgtgagtttgtatttatttgatttgatgttgagttgctaactaactacacttaaatatctagGCTTGCAAAGAAATGGGAAGAGCTGCAGACTAAGGTGGATTAACTACTTGAGGCCAGGATTGAAGAGAGGGGTGTTCAGCAAACATGAGAAAGATACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - tatgtag
- - - - - - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacact