Sequence
atgc intronic sequence ATGC exonic sequencegtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtgtagtgttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
Basic information
species | Glycine max |
transcript | GLYMA02G45030.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g05050.3 (Oryza sativa), 3'ss of exon 1
gtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtg--tagtgttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
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-----------------------------taatttgcaatatgatttgcttggtgctcttgtcactctactttatttttcttttttttgcttttttat-gtagtgatgtgttttatctttctctgtccagAGGGCTGTCCTTGATCCAGCAATGCAAGGCAAAGATATGATTGGACGTGCAAGAACTGGAACTGGGAAAACGTTGGCTTTTGGTATTCCTATCATGGACA
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtgtagtgttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
|| ||| | | | | ||||| ||| ||| || ||| | ||| || ||||| ||| || | || ||| || | || | |||| ||||||||||| || || ||| | ||||||||||||||||| || || || |||||||| || ||||| |||||||||||||| || || || || |
-------------------gtatatatgatcttcttctctgttccatttggtt-atagagatcaattaaaagtttagatttttttaact--gagtttttgatgtttgtgtt---tggttga---atagAAAGCTGTGTTGGAGCCAGCGATGGAGGGTCGTGATATGATTGGCCGTGCAAGGACTGGAACGGGAAAGACACTTGCTTTTGGGATTCCTATTATTGACA
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtgtagtgttg--atgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
| | | ||| | |||| || | | | || | | ||||| ||||| | | | | |||||| | | | | |||| |||||| |||| || || ||| | ||||| |||||||||||||| ||||| |||||||| || ||||| |||||||||||||| || ||||| || |
------------------------gtatgtaatgtt--gtgagatcaaaattttaaattgttcagcttttcgtgttcccatgtttttggaagaagggtaagtgggttttaagttttgtggttttgagtagAAAGCTGTGCTGGAGCCAGCGATGGAGGGTCGAGATATGATTGGTCGTGCTAGGACTGGAACGGGAAAGACACTTGCTTTTGGGATTCCTATCATTGACA
upper sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 1
gtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtgtagtgttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
| || || || |||||| ||||| || ||| | | || | | | | ||| | | | ||| || | || | || | | | |||| |||||| |||||||||| |||||||| ||||| ||||| ||||| |||||||| || |||||||| || |||||||||||||| |||||||||||||
--tcatgttaattgttcacatttatttcttgatat---------------gtcagtaact--caatat------tcggttttggagattcc---atttttcgtaaaaaaaaatttgtacattgtacagAGAGCTGTGCTGGAACCTGCAATGCAAGGGCGTGACATGATCGGTCGTGCTAGAACAGGGACTGGGAAAACCCTTGCTTTTGGGATTCCCATCATGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
ttttt CT-rich tract
ttcgagattgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctttgcttcctctggtttattctttgatgcaaaatatgatccgtggttgataattatcgatgtgtagtgttgatgttgataacttcgagattgttattttttaattaattaattaatttttagAGGGCTGTGTTGGAACCTGCTATGCAAGGTCGTGATATGATTGGTCGAGCTAGAACTGGAACTGGGAAGACTCTTGCTTTTGGGATACCCATCATGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA