Sequence
atgc intronic sequence ATGC exonic sequence...atttttctttgatgattgaattgaagagatcagagtatatataactttagtttactaagtggcattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
Basic information
species | Glycine max |
transcript | GLYMA06G10540.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 8
atttttctttgatgattgaattgaagagatcagagtatatataactttagtttactaagtgg-cattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
| || || | | | ||| | ||| | | | || | || || || | | | || | || ||| | ||||||||||| ||||| || ||||| || ||||| || ||||| || ||||||||||| ||||| ||| |||| ||||||| |||| ||||||
--------------------gtaaacttat-acactttatccatgcttaatatccatcgtagtcaccatcaga-gtgactttctctcttctcaattgaaagGTCAATACATGGGGCTATTCTACGATAAACTTTTTTGCACCCATGAGCCGTTATGCTAGTGCCGGTGGTGGACCAGTGGCTGCTTCCAAAGAGCTCAAGC
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 8
atttttctttgatgattgaattgaagagatcagagtatatataactttagtttactaagtggcattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
| | || | | || | |||| | || | |||||| | | | ||| |||| |||| ||| | ||||||||||| ||||| ||||| || || ||||| || |||||||| ||||||||||||||||| ||| | || ||||||| |||| |||| |
-------------gtaaaagtttgataacctttttgatgcagcacttcaaattcatcagtggcgtgacaccccacc----------ttttcatttcaaagGTAAATACATGGGGATATTCTACAATCAACTTTTTTGCGCCCATGAGTCGTTATGCTAGTGCTGGTGGTGGACCTGTGGCTGCTTCCAAAGAGCTCAAAC
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G385578_T01 (Zea mays), 3'ss of exon 6
atttttctttgatgattgaattgaagagatcagagtatatataactttagtttactaagtggcattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
| |||||| | | || | | ||| | || || | | | | | | ||||||| || ||| |||| ||| | ||||||||||| ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| ||| | || ||||||| ||||||||| |
gtaaaagtttgataaccttttcgatggg-tcattaccccctcacattcagc--agtg-gcgtgagtgcgtgacactcccactt----tttcatttcaaagGTAAATACATGGGGATATTCTACAATCAACTTTTTTGCACCCATGAGTCGTTATGCTAGTGCGGGTGGTGGACCTGTGGCTGCTTCCAAAGAGTTCAAAC
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 8
atttttctttgatgattgaattgaag-agatcagagtatatataactttagtttactaagtggcattatatgacactg-atggttgtatttttttttcc--aagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
|||| | | || | ||| | ||| || | | ||| || ||| | || |||| | ||| || |||| | ||| |||||||| || ||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| | |||| |||||| | ||||||||
--tttttatggcatatagcattatctcatgtcatagc-tttctaagtt-gccttatttggtattcatatacattatgatatgttttcatttctgaatcccaaagATTAACACGTGGGGATATTCAACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGACCTATTAAAGCTTCCAGGGAGTTCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagtttactaagtggcattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
cactgat putative branch site (score: 3)
ttgtatttttttttcc putative PPT
ttgtattttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttctttgatgattgaattgaagagatcagagtatatataactttagtttactaagtggcattatatgacactgatggttgtatttttttttccaagATTAATACATGGGGTTATTCGACAATAAATTTCTTTGCTCCTATGAGTCGCTATGCTAGTGCTGGTGGAGGATCAGTTAATGCTTCCCGAGAGTTCAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg