Sequence
atgc intronic sequence ATGC exonic sequence...attctctccctccccccttctcccaatttacatacaagggatttttttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
Basic information
species | Glycine max |
transcript | GLYMA17G05410.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------------attctctccctccccccttct---ccca---atttacatacaagggatt---tttttcctcac---aatcagatgtagca-gttatactct-------ctattctgattgctat--att-cagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| ||| || |||| ||| | || | ||| | || || | | |||| ||| | | | || ||| | | | | || ||| | | || ||| |||| |||||||||||||||||||| ||||||||||| || || |||||||||||||| || |||||||| || || |||||||| ||| | ||||||||
gtgagttcaaacgaaaacttctactactatatattttaatttctagcaatttgtttctcaaccagttcctcaccttccctacttttatattcatacaattatcttcatggtctccagtgtttcaccactggagtaaaataaagcttatcacgcatttagaatgcttctctaagttctcccgattatagGTTATGCATCTTGATGCTGAAAAGGAGATGATGTCCCAGTGCGTGGCTCTTCTTGGGAAGTTTATTGCAGTTCGGGAACCAAATATTAGGTATCTTGGTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 9
attctctccctccccccttctcccaatttacatacaagggatttttttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | | || | || ||||| || || || | | | | || | ||| |||| | ||| || |||| |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || |||||
gtgagtttgtacttatgtttcgcaaaattaca-gtttggtatattgtctttttaattaagtctttgcacgtataat-------------gcttcatatagGTCATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 8
-----------------------------attctct-ccctccccccttctcccaat---ttacatacaagggatttttttcctcacaatcaga-------------tgtagcagttatac---tctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
|| | | |||| || ||| || | || | || | || | | | || ||||| | | || | ||| | | || | | || || |||| |||||||| |||||||| || ||||||||||| || ||||||||||||||||| || |||||||| ||||| || ||||||||||| || || ||
gtgagtttgtattgactttaaagcgattaatcccccaccctggtccgatcttgcattgccttttctgcataagtttatgcttcgcaaaatcacagtttggtatcctgtctattaattaagtctgtttgcatgtataatactccatatagGTCATGCATCTGGATGCTGAGAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTCGGTC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
-attctctccctccccccttctcccaatttacatacaagggatttttt-tcctcacaatcag-atgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
||| | || || || | | | ||| | || || | | ||| | || | || || |||| |||| ||||||||||||||||| || || |||||||| || ||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtg-ttttgatat--agGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 8
------attctctccctccccccttctcccaatttacatacaagggatttttttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | | | || || || || | | || || | | || | | || ||| || | || || |||| |||| ||||||||||||||||| || || |||||||| || ||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
aagagagcttttcttcgcgatgattagattgatgagcacactctag-taaactttctggct-tagtgtgcaaccccta-acttgttaatgtg-ttttgatat--agGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 8
attctctccctccccccttctcccaatttacatacaagggattt-ttttcctcacaatcagatgtagcagttatac---tctctattctgattgctatatt-cagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| | || ||| | |||| | | ||| | | |||| | | ||| | | ||| |||| | | | | ||| | | ||||| |||||||| |||||||||||||| ||||||||||||||||| || | ||||| |||||||||||||| || || ||||| || ||||||||||| |
---gttgggttttcctcttatttcaatgtgggtttaagatactggtttttatgagaattaa--ggagcttttatgtggttgtgtccttcaattaccctggcacagGTCATGCATCTGGATGCTGAAAAAGAAATGATGTCTCAATGTGTTGCCTTGCTTGGGAAATTTATTGCTGTACGAGAGCCAAATATACGATATCTTGGTT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 8
attctctccctccccccttctcccaatttacatacaagggatttttttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
| |||||| | || | ||| || | | | | || | | || |||||||||||| | || || || ||||| |||||| | |||||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||
------------------------------------gtaggttttttctttt----tctgttgttccattcaagagccttttttttgtcgcg-----cagGTGATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
tatattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attctctccctccccccttctcccaatttacatacaagggatttttttcctcacaatcagatgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
- tctctcc
- - - - -ctccccc
- - - - - - - - -ttctccc
- - - - - - - - - - - - - - -acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg