Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
Basic information
species | Glycine max |
transcript | GLYMA09G03590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g20180.1 (Oryza sativa), 3'ss of exon 5
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
|| | || || | | ||||||| |||| | ||| | || | | || |||| ||| | | ||| |||||||||| || |||||||||||||| || || || ||||||||| | ||||||||| |||| | ||||| || |||||||| ||||| ||| ||| |
------------------------------------------gtgagtgttgatgagtcctcttttttcttttcttt-----tcataaaattgttatttgtg--aatttgacttac-taacacttatacttt------agGTTAATGCTAGCGGGCAGTTCTGTGGTGTTGCTGAAATGGTTGGTCCTGTTGATTTTCACAAAGACATGGATTTCTGGCAGCAGGATAAGTGGTCTGGGA
upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G056573_T01 (Zea mays), 3'ss of exon 6
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
|| | || || | || | | || | ||||| || ||| | | || | |||||||| ||| ||||| | ||||| |||| |||||||| |||||||| | || |||||||||||| | ||||||||| ||||| | |||||||| ||| || |||||||||| ||
------------------------------------------gtgagtattgatt-tattgaacatccataaaatttatcatgctta---aagttcaaca-attgacttttttta----atgtttat----------cagGTGAATGGGAGTGGGCACTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCACAAGGACATGGACTTCTGGTGTCAGGATAAATGGACCGGCT
upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
| |||||| |||||| | || |||| |||| | | | || || || |||||||| | | |||||||||| ||||| ||||||||| | || |||||| |||| ||||| |||| | || | ||||| |||||||||||||| |||||||||||||
----------------------------------------------------------gtgagtttttcc-ttctctctt-tttacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctt--tttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G17330.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagc-taatcacactgacttttctta-tgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
| | | || || | || || | ||| | ||| ||| | || | || | ||||| ||| | |||| ||| | ||||| | ||||||||| || || |||||| ||| ||||| || || | ||||| |||||||||||||| |||||||||||||
----------------------------------------------------gtgagtcgattcttcccctttgtcccttgtgcgaatgtgtttgcattcatactttgtgctcatgctgatgtagtgcttccttcgttttagGTCAATTCCAGTGGTCTGTTCTGTGGCGTGGCTGAGATGACCGGTCCAGTTTCCTTCGACCGAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
upper sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttat--aattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
|||||| || | || | | | | || | | || | | ||| | | |||| | | | |||| | | | | || | | | || | | | ||||||| | ||| | || ||||| |||||||| || || |||||||| || ||||||||| |||| | |||||||| | ||| |||||||||| |||||||||||||| ||||||||||
gtgagt-tttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaa----tttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
cactgac putative branch site (score: 2)
ttgcttttttc putative PPT
ttttcttatgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA