Sequence
atgc intronic sequence ATGC exonic sequence...tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
Basic information
species | Glycine max |
transcript | GLYMA11G06650.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
---tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
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aataattgacatgtgaaagtt--gttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatc-ttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
upper sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactag------------aattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
|| || | | | || | | | | | | | || || | || || | || | ||| || || ||| || |||| || || ||| |||||| ||||| ||||| || |||||||||||| ||||||||||||| || |||||||| | ||||| ||| | | || |
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaa--taaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
upper sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
--tcttcatgaa--cagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
| || | ||| ||| | | | | ||| ||| || | | || || ||| ||| | || | |||| || | | || | |||| ||| | ||| || |||| | ||||||||||| |||||||||||| | ||| | ||||| || |||||||||| |||||| ||| |||| ||||
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttca-caaatgatactgtagcattaa-tgtaattctt--tcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
upper sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
---tcttcatgaac-agaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
| | || ||| ||| | | | | ||| ||| || | | || || ||| ||| | || | | || || | |||| | |||| ||||| ||| || |||| || |||||||||||||| ||||| |||||| | ||||| ||||| || ||||| |||| |||||| ||| |||| ||||
tattttgaataaactagatgtgcaatgtatatttgtttcttttgtatgtttttca-caaatgatactgtagcatcaa-tgtatttctt--tcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
ttggttctttcctt CT-rich tract
taaactagaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - catgaac
- - - - - - - - - - - - - - - - - - -aaaaaaa