Sequence
atgc intronic sequence ATGC exonic sequencegtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
Basic information
species | Glycine max |
transcript | GLYMA09G01830.1 |
intron # | 5 |
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 5
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 5
gtgtggttattctgttatgtgatgttgaaatt-catggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
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----------tttgtcacatagccatattactgcacaaccaagttagacattaagatctttttttttgtctgtgaactt--gcatggtagctgacgcttgtgtctgtt-----gcagGGCCGCCTGTTTTTATCTCCAAGAATTATTGGGTTCTACACTAATCTTTTTGGCCACAAAACAAAATTCTTCTTTCTTTGGGAAGATATCGAGGACATCC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G005195_T02 (Zea mays), 3'ss of exon 5
gtgtggttattctgttatgtgat-gttgaaattcatggtcaattattctactttggtttttac-tggtgcatgcttcttttagtatcttctcataaaattgtgaatatttct-ctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
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------------------gtgattacttaagggcatcactg-ttactttacaacaaactaagcataaccttttcatgtcatcatgcctgagaactaaatcatgtctgcctgtgttgcagGGTCGTATTTTTCTATCTCCAAGAATATTTGGGTTTTACACAAATCTTTTTGGCCACAAAACAAAATTCTTCTTTCTTTGGGAAGATATTGAAGACATCC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G027665_T01 (Zea mays), 3'ss of exon 5
gtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttct-ctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
||| | ||| | | | || | | |||||| ||| ||| ||||| | | || | |||| || | | | ||||||| || || |||||||| |||||||| |||| ||| | ||||| | ||||| |||| ||||||||||| || |||||||||||||||||||| |||
----------tctaatcaacgatt-----acttaagggtataactgttactttacaacaaactca-acataacctttttatt-ttatcaaactaaatcatgtctgcctgtgttgcagGGTCGTCTTTTTCTATCTCCAAGAATATTTGGGTTTTACACAAATATTTTTGGCCACAAAACAAAATTCTTCTTACTTTGGGAAGATATTGAAGACATTT
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------gtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
||| | | || | | | || || ||| || | || ||||| | ||| | | | || | ||| |||| | | | | ||||||| || || || || || |||||||| |||| ||| |||||| | ||||| ||||| |||||||||||||| || ||||||||||| || |||||||
gtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataaca------catgtaattaagttt-tacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 5
gtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
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------ttaagctgtctttgga----gaaattagatatggatatttttgccct----cttacaggtttaaa--tattgaatgctctttacatttgacctcacttgttttcatgcagGGACGGTTGTTTATGTCTGCAAGAATAATTGGGTTCCATGCAAATTTATTTGGCCATAAAACAAAGTTCTTTTTCCTCTGGGAGGACATAGATGACATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
tatttctct CT-rich tract
ataaaattgtgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA