Sequence
atgc intronic sequence ATGC exonic sequence...ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 9
ggcagagcatgctatgtaattcattttt-----ttttacttttgtttggat-tccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
|| || |||| | | | | | ||| |||| | | | | || | | || | || | | | | || ||| | || ||| | ||||| || || ||| | ||||||||||||||||||||||||||||| |||||||||||||| |||
ggtgatttatactattttctgtagccatagaggtgttatttttctgcagctgttacttcgatgtttttgt---gttcatataaattttttc---cttttgttccagCTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 9
ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtc---tcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
| | | ||| | | || | || || | | | | || | | | |||| || ||||| | || | | | ||||||||||||| || || |||||||| || ||||||||||| ||||| ||||| || |||||||| || |||
---aaacttttatatattctgcagctgattctaatactacgtatcatataagtggtatactgcttgaaatgtcattagtccgttgctccttttctttcttcagTTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 9
ggcagagcatgctat-gtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtctcat-ctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
|| | || |||| | || | | || | | || || | ||| | | | || | || |||||| |||| ||| | ||||| | || ||| |||||||||| |||||||||||||||||||| |||||| ||||||| |||
--cacattatactatcgctatctttctccagaaacataaacatactatcactaagatttgtttcatgtgtttttgctcatactatactgtctattattacagCTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 9
ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtt-------tttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
| | | | ||| | || | | | ||| | |||| ||||| ||||| | | | ||||| |||| ||| | ||||| | || ||| |||| |||||||||||||||||||||||||| |||||| ||||||| |||
-----accgcattttactatta--tcttctacagaatcaaacaaattatcactgtaaaatttgtttatgtgtttcttcccatacctatactttgtctactattacagCTTTGGGATGTTAAGATGAATTCCGGTCCAGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
------------------ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
|| |||| || | | ||| || ||| ||| | |||| | | | ||| | | | || || || || ||||||||||||||||| ||||| | |||||||| ||||| ||||||||||| || ||||| | ||||||
gtccatattttcactgttttcatcattcaatatgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttat--gttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
--ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagt-ctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
| | |||| | | |||| || | | | | | || | | | | ||| || |||| | | | | |||| ||||||||||||||||| |||||||| || || |||||| |||| ||||||||||| || |||||||| || |||
aggtctttgcatcacaaggaattgatatgtactatttgtctttctggcttaagttagggccttgaactaa---tcactggaatttgttttacttgcttttcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
tctgtctt CT-rich tract
tttttatcaacaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG
- - - gcatgct
- - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgt