Sequence
atgc intronic sequence ATGC exonic sequencegtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
Basic information
species | Glycine max |
transcript | GLYMA16G20260.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g68750.1 (Oryza sativa), 3'ss of exon 5
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataaccaataataccttgttctt-----tgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
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gtgacagcatcagtctatgcatgtt--tgttgttgagcacttaatgtattttctactaatatttttaacagaagatcctttggttctactaattatttaccagACCATGAACAAAGTCTTTGAGCATGCTGGAGATCTTGTCAACATCCGAGTTGCACATAATTTAATGCGACTTATTGCTGAAGGCTTTGGAGAGGAGGATG
upper sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 5
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataacc-aataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
|| ||| | || | | | ||| | | | | |||| | | || | ||| ||| | | || ||||||||||| ||||||||||||||||| ||||||||||| || || | ||||| || ||| | ||||| | |||| |||||| ||||||||||| ||||
--------gtaatcacatgagtattgtccaacat--attgtcaagcatcctttgttgcttcttgagagctgaactctttcttcctctattttcttacagACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTGGCGCACAATCTGATGCGGCTAATTGCTGAAGGCTTTGGAGAGGAGGATG
upper sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 4
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataacc-aataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
| | | | | | ||| || || ||| | || || ||||| |||| | | || | ||| ||| | | || ||||||||||| | ||| ||||||||||||||||||||||| || || | ||||| || ||||| ||||| | |||| |||||| |||||||| || || |
-----gttatcacatgagtattgtcctaaatattg--tcatgcatcttttgt---tgcctcttgagagctgaaccttttcttcctctattctcttacagACCATGAACAGAGTTTTTGAGCATGCTGGAGATCTTGTCAACATCAGAGTGGCACACAATTTGATGCGGCTAATTGCTGAAGGCTTTGGAGATGAGGACG
upper sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
||| | | || | || | | || || | | | || || | || | | |||| | | |||||| ||||||||||||||| |||||||| |||||||| || |||||||| ||||| |||||| | ||||| ||||||| |||||||||||||||||| ||||
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatat----actctttgtttctgacagaagtttaactgtttct--gtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
upper sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 5
gtaatggtgttgctgcatttat-gttcttgattttgaattatttatgt-tttgcaaacattcattgataaccaataataccttgttctt-tgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
||||| | ||| ||| ||| ||| |||| | || | | ||| || | | | | | | || | ||| || ||| |||||||||||||||||||||||||||||||||||| | || |||||||||||||| ||||||| ||||| ||||||| || || || |||||||| ||||
gtaattatattgttgccttttccattccagattgtatatgaacgggttgcttgtgtttttttaccttttaatgcttagattttctccttatgtgtttacagACCATGAATAAAGTCTTTGAGCATGCTGGAGATTTGGTCAATATTAAGGTGGCTGATAATTTGATGCGGTTGATTGCGGAGGGGTTCGGAGAGGACGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
ttctttg CT-rich tract
tttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG