Sequence
atgc intronic sequence ATGC exonic sequence...cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC
Basic information
species | Glycine max |
transcript | GLYMA18G45200.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 2
-------cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-
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tttcgggcatattattaacttggaaatccttaccttttcattcttgtcgttatgttataagaatt---atcaggaagtaactcatcttt-tgtttctttgt----cagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA
upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 2
cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-
| ||| || | | | |||| | ||| || | | | || ||| || | ||| | | | || | ||||| ||||| | || || |||||||| || ||||| ||| | || |||||||||||||| |||||||||||||| ||||||||||||||||| ||||||
ttcgggcatattattaact-tggaaattcattaccttttcattcttgtcgttatgttagaagaattatcaagaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA
upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
cgtgatg-tgattgttgagtgtcaaaa----taccttaatgttgaaatt-gcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-
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tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaa---atgttttatccatcttttgtgtttatgt----cagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 2
-cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtg-caGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-
|| | || | | | | | || | | | | || || | | | | | | ||||| ||| | | | || | | || ||||| || || || | || |||||| | |||||||| || ||||||||||||| || || |||||||||||||| || |||||||||| || ||||||
ctgtaaaatgctattgggttatttttgcacat-ggtttgacagttatcatgcttgttactagcctacaaaattatt--attctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-
|| | | || | | || | | ||| | | | ||| | || || ||| || || ||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| ||||| || ||||| || |||||| || |||||||||| |||||
-------------------gtaagcttgtgtttttatcttctttctttgg--tgggttggtgctttgactgatttttttactgggtctttacgtc-tgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC
atttaat putative branch site (score: 4)
tttatttaattttgtg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- tgatgtg
- - - - - - - tgagtgt
- - - - - - - - - - - aaaatacc
- - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - -tgcagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt