Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatcatgtcatcatttattattttttgttttacaacttggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgtattttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
Basic information
species | Glycine max |
transcript | GLYMA09G01830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 3
gtgagtatcatgtcatcatttattattttttgttttacaacttggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgtattttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
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----------------------------------------------gtaaaagtttggctt--attatcttatgttataattgc--tgctatataaaattacaattcataatttt--gcaacatatcttctcaaaatttgcagAAATTTTTGAATTTGATGCCATGGAAGATCCTCCATCCGTTATGAAAATAAATGTCTACGATTTTGATGGACCATTTGATGAAGTTGAGTCTCTTGGTCA
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G179351_T01 (Zea mays), 3'ss of exon 4
--gtgagtatcatgtcatcatttattattttttgtt-----ttacaacttggatcaaac-ctctgaattcggtgatctaatgt------agttttcccaacacacta--tgtattttatattattgttttttggttaagaacaat--gtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
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gtatacattttctgcgactgtttctggcttcttcttaaaccttgtcatctgcttccatcactaggaaattgtaaatttgaactgcaccaaattttagtagcatagaaacagtgtgttttgttat-gccatgcaactaaacctagttcaccaaatcttgcagAAATCTTTGAATTTGACGCAATGGATGATCCACCGTCGGTGATGAGTGTACATGTATATGATTTTGATGGACCATTCGATGAAGTTACATCCCTTGGACA
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtgagtatcatgtcatcatttattattttttgttttacaacttggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgtattttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
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gtaaatggttactctatggtttttatgtctagttatcttagtggtagcatggtcttatcctcaagctgacttttcatccacttgttttcgtcaattcttgaatgtttcaactctttgtttttttg--agggtggaattttgtttgtgcagAAATATTTGAATTCGATGCAATGGCTGATCCTCCTTCTGTACTGAATGTTGAAGTTTTTGATTTCGATGGACCTTTTGACGAGGCTGTTTCATTGGGGCA
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------gtgagtatcatgtcatcatt-tattattttttgttttacaact--tggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgt----attttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
| | || | ||| | | | |||| | | | | ||| | | | | | | | | || | ||| | | ||| ||| ||||| | | |||| |||| | |||| | | ||| ||||| |||||||| ||||||||||||||||| ||||| ||| |||||||||||| ||||| |||||||| |||||||||||||||||| |||| || || ||
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggctt-gcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactatgtattttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
tctatcttt CT-rich tract
tattttatattattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatcatgtcatcatttattattttttgttttacaacttggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgtattttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC