Sequence
atgc intronic sequence ATGC exonic sequence...aaaacttatctgatctttgtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
Basic information
species | Glycine max |
transcript | GLYMA17G09020.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 8
aaaacttatctgatctttgtcatgaaattatgatgctaagtgca--agtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
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----------------------gtaagttatgcttcagatttcaccaatttattagcagcagagtttcgttatgtattggttgttgttatt-tgaact--agGATGTGGCGGGAAATTCGACTCCTAGCTGACACCAAGCCTGTGGTTGCTTCAATGTCTGATGTTGCTGCAAGTGGTGGGTACTACATGGCAATGGCTGCA
upper sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 13
aaaacttatctgatctttgtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
|| ||| | | | | | || | || || || | | |||||| | | | ||| | | || || | | |||||||||||||||||| | ||||| || ||| ||||| || ||||||| ||||||||||| || |||||||| || |||||||||||||||| |||
gtaagttac--gccttaggatttagtgatttgcttctcagcagcagcagca-gcagagttttttcagtaacatattacgaattcttatttcaact---agGATGTGGAGAGAAATCCGACTTCTAGCCAACTCTAAACCTGTAGTTGCTTCGATGTCTGATGTTGCTGCAAGTGGGGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
aaaacttatctgatcttt--gtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttg-tttaactataaagtt--ttgtt-gtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
| ||||| || |||||| | || | | | || ||||| | | || | || | ||||| || || || | ||| | | ||| |||||||| || |||| || ||||||| ||||||| |||||||| |||||||| |||||||||||||||||||| |||||||||||||||| |||
--tatctatctagcctagaggtcatg----tgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 4
aaaacttat-ctgatctttgtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttgtttaactataaagttttg-ttgtcatgatc-tgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
||| | | ||| ||| |||| | | | || | || | || || || | ||||| ||||| |||||||| |||||||| |||||||||||||||||||| |||||||| ||||||||||||||||| || || |||||||||||||||||||||||||||
---gcttgtacagatgaaaaaagagaaggaatgagaaaagaaaaatgcatgacaaatataatgagctcccactaattggtccttaatttttatgattatgcagAATGTGGAGGGAAATCAGACTTCTGGCTGCCTCAAAACCTGTCATTGCATCAATGTCTGATGTGGCTGCTAGCGGAGGGTACTACATGGCAATGGGAGCA
upper sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_21V6.1 (Physcomitrella patens), 3'ss of exon 11
----aaaacttatctgatctttgtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
|||| || || ||| || | | || | | || || | ||| | | ||||| ||| ||||| | | | ||||||||| | ||||||| || || |||| ||| ||||| ||||| |||||| | || || ||||| |||||||| |||||||||||||||| |||
cgtaaaaaagctgcttataactgtattgttgtcagtgcatcaattacg----ttaccgttttcctacttctgaacttataatttttcgttgttacggccattagGATGTGGCGGGAAATCAAACTCCTAGCTGAAAGAAAGCCAGTGATTGCATCAATGGCCGACGTAGCAGCTAGTGGAGGCTACTACATGGCAATGGCAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
gtttaac putative branch site (score: 3)
tttaactataaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaacttatctgatctttgtcatgaaattatgatgctaagtgcaagtattttggtgagtttgcttgtttaactataaagttttgttgtcatgatctgcagGATGTGGAGAGAAATCAGGCTTCTGGCTGCCTCAAAACCAGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA