Sequence
atgc intronic sequence ATGC exonic sequencegtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
Basic information
species | Glycine max |
transcript | GLYMA20G32430.2 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
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--gtttggaatgt---ctagttttgcattatactt---tatattattcatttgcagttataatgacacagatattttctatttgtta--tgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 26
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttc-tatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
||| || | || | ||| ||| || | | ||| | || | | || ||| | | ||| | ||| || |||||||| || | ||||| |||| |||||||||||||| |||||||||||| ||||||| ||| | | |||| | ||| | ||||| | || |
--gtttggaactaactcccatgttat-ctttactcctgcatgcttttatttggtcgctaccataactgacaactgtttgt--ttgtta--tgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCATGGATTGCTGCAGCCCAAC
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
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--gtttggaactcactcgcatgctatctatttttct-gcatgcttatttttggtcactacaataattaacaactgtttgtttg---tcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
lower sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgtttt-gccgttttcta-----tttgaatatttcttgaaatggtttgtt-gcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
| | || | | | ||||| ||| || || |||||| | | || || | | | || || || |||| || |||||| ||||| |||||| | ||||||| ||||||||||| || ||||| ||||||||||| ||| ||| |||| |||||||| |||||||||||||
------gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
ttttctatttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT