Sequence
atgc intronic sequence ATGC exonic sequence...agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattattgttaaaatgtttcaaaagtgatcaaagttttaaacttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
Basic information
species | Glycine max |
transcript | GLYMA03G27490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 2
agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattattgttaaaatgtttcaaaagtgatcaaagttt-taaacttg--tgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
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--cggcttttcagaccatgacaacaaaacttgtagaatagacttgtgatctact-tagttttagtacttttaagatgaagattcttggtaatgttacttgtagGAGCTCAACCATGCCGGGGCTGGTGGACTGTGGGCAGAGCTTGTAAGCAACAGAG
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 3'ss of exon 3
agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattattgttaaaatgtttcaaaagtgatcaaagttttaaacttg--tgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
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tgcaacattttcctatatatagtacctgcatatcaaatgaggt-tgcttcgacttctattcca-tgctgggagcttgaatatatttgtggttctacttgtagGAGATCAACCATGCTGGGGCTGGTGGGTTGTGGGCAGAGCTTGTAAGTAACAGAG
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------agtttcc-tttcacaatgcatggttatttttaactagatgatatctttttttattattgttaaaa--tgtttcaaaagtgatcaaagttttaaacttg--tgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
|||| || || || || ||||| | | | |||| | ||| ||| || | | || |||| | | |||||||||||||||| || |||||||| |||||| ||||||| || | ||||||||
gtgcgagtcagattacaattgtgctatcagttagaagcagcagttcatctgctggcacatcaacagttcaaattctgaaaccaatttttgtttttgatttctatgctctgatggttatcctgagaaaagattgtgggtaactcggttaagtttttggttgtacctatagGAGATCAACCATGCTGGAGCTGGTGGGTTGTGGTCAGAGCTCGTAAGCAACAGAG
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 2
agtttcctttcacaatgcatggttatttttaactagatgatatctttttt-tattattgttaaaatgtttcaaaagtgatcaaagttt------taaacttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
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-----------gtgaggca--gtagtttatcggtagatgctagttcctatgttttaccacatataatcagaaagaataatccaaatatactgcatggcctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
agtttcctttcacaatgc-atggttatttttaactagatgatatctttttttattat-tgttaaaatgtttcaaaagtgatcaaagttttaaacttgt-gcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
||| |||| | ||| | || ||||| | | | | || |||| |||| ||| || | | | | || | | |||||||||||||||| ||||| |||||||| ||||| || ||||||| ||||||||
------gtttgttaatgttacggtc----tcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
upper sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattat-tgttaaaatgtttcaaaagtgatcaaagttttaaac----ttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
| | |||| ||| | | ||| || | || | | || ||| |||| | ||| || | ||| | |||| ||| ||||| |||||||||||||||| || ||||||||| |||||||||||||||| | ||||||||
-gggttgtttcg-aattctgagcaattagcaatttactgccactgtaattgtgtatatgttgat---tttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttattattgttaaaatgtttcaaaagtgatcaaagttttaaacttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
tattattgttaaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattattgttaaaatgtttcaaaagtgatcaaagttttaaacttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -cctttca
- - - - - - - - gcatggt