Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctcaatttctcatgcaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
--------------------gtttgtctcaatttctcatgcaataat-tatccctccctgac--ttattgttactgacatagg-atgtggaatgat--agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| | | | || |||| ||| |||| | | | | | | ||| || || | | || |||| || |||| ||||||||||| ||||| |||||||| | ||||| |||||||||||||||||||||||||| ||||
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
--------------gtttgtctcaatttctcatgcaataattatcc-ctccctgact--tattgttactgacataggatgtgg----aatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
| | | || | | || ||| |||| || |||| || ||| | || |||| ||| | | ||||| || | |||||||| ||||| ||||| ||||| || | |||||||||||||||||||||||||| ||||| || |
gtatgttgaaacaaatgaattaccatgctttgttcag-aataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
---------------gtttgtctcaatttct--catgcaataattatccctccctgacttat-tgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| ||| | | | || || | | || | || || | | | | ||||| | | |||| || |||||||||| ||||| ||||| ||||||||| | |||||||| ||||||||||||||||||||||||||||
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
--------------------------gtttgtctcaatttctcatgcaataattatccctccctgactta---ttgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| ||| ||| | ||| ||| | | | | | ||| ||| | | | | || ||| |||| ||| ||||||||||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctcaatttctcatgcaataattatccctccctgac--ttat-tgttactgacataggatgtg------gaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| || ||||| | |||| || | | |||| | || | | || || | |||||||| || || || || || || |||||||| ||||| || |||||||||||||||| || ||||| ||||||||||| |
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctcaatttctcatgcaataattatccctccctg-acttattgttactgacatagg--atgtgga---atgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
|| || | | || | || || || ||| | | | | || || || | | || | | |||||||| || | || || || ||||||||||| ||||| || |||||||||| ||||| |||||||| ||||||||||| |
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------gtttgtctcaatttctcatgcaataattatccctccctgactt--attgttactgacatag-----gatg-tggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||||| | | | | | ||||| | || || | || | ||| | || | | || || | ||||| || ||||| || || || ||||||||||||||||||||||||||||||||||| || || || ||||| ||||| |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaa-acgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------gtttgtctcaatttctcatgcaataattatccct-------ccctgactta----ttgttactgacataggatgtggaatgat-----agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| ||| |||| | | || || | || || | |||| | | | || || || | | | |||| || || || ||||| || || |||||||||||||||||||||||||||||||| || || || ||||| ||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtctcaatttctcatgcaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
| || || |||| ||||| |||| | || || | |||| |||||||| || || || || |||||||||||||| ||||||||||||| ||||||||||| || || |||||||
---------------------gttggttgtcttcgtttgacaa---gttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtctcaatttctcatgcaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
| || | |||| ||||| |||| || || | |||| |||||||| || || || || |||||||||||||| ||||||||||||| ||||||||||| || || |||||||
---------------------gttggttgttttcgtttgacaa---gttacatacatgactcttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
tactgac putative branch site (score: 1)
ttattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctcaatttctcatgcaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA