Sequence
atgc intronic sequence ATGC exonic sequencegtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
Basic information
species | Glycine max |
transcript | GLYMA14G37510.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
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----------------gtagttaactactcctgatgttgatatgtgcgaagcaatttt--gtcct--taacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
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----------------gtagttaactacacctgatgttgatatgtgcgaagcaatttt--gtcct--taacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtct---tgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
||| || | | | ||| | |||| | || | | | | | || | | ||| || ||| | | | | | ||||||||||| ||||| || ||||| || || ||||||||||| | ||||||||| || || || || |||||||| || | || || || || ||||||
gtagttactct----tactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
gtatttctt--aagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
||||||||| || || | | |||| | || | || ||| || | | || ||| || |||| | || ||| || |||| ||||| |||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||
gtatttcttttaataaaagaaaaaactgactttaatttt-------aagcatt----------ttttgtatattttcttatttttcaccttc-attttg----agacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattc--tgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
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-------------------------------------------------------------gtatatccgtggttttaaaattg-catgtaatcaagtgtcttgtgcagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttatt--ctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
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-------------------------------------------------------------gtatatccgtggttttaaagttg-catgtaatcaattgtcttgtacagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
ttctaat putative branch site (score: 2)
ctttttattctgtctt putative PPT
ttctatttacttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG