Sequence
atgc intronic sequence ATGC exonic sequencegtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
Basic information
species | Glycine max |
transcript | GLYMA20G38270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
-------------------------gtatggtgtaatctttatattcctttctaatcaggactttttaactag----cctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
| | | || |||| | || | | ||| | | || || | || ||| | || ||||| || ||||| | |||||||| ||||||||||||||||| ||||| ||||| || || ||||| || || || ||||||||||| |||||||| ||||
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G836628_T02 (Zea mays), 3'ss of exon 3
-------------gtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
|| | |||| || || ||| | | || | | || || || | || ||||| || ||||| || |||||||||||||| |||||||| || ||||| || || |||| ||| || ||||| || |||||||| || |||||||| ||||
gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatcaattcctgcatgaatgcttatg-----ttgggggactt-tagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G113016_T01 (Zea mays), 3'ss of exon 3
-------------------gtatggt-gtaatctttatattcctttctaatc-----aggactttttaactagcctgttttg-gttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
|| | | |||| | ||| | |||| || | || | ||||| | ||| || | ||| ||| || ||||| || |||||||||||||| ||||||||||| ||||| ||||| |||| ||| || || || | |||||||| || |||||||| ||||
gtaaaccagttcaattcgagtcagttagtaacttccttatcctcaatcaatcgtacgagcatcttgctgatgcactgttgtatgtttttttgggaaatta--gGTTGGTCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTTTCAAGATCCATTGGGGACATGGATGTTGGGGAGTACATTGTGCCCATTCCACATGTCAAGC
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
-------------------------------------gtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttat-agGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
| | | || | | || | || | ||| | | | | |||| || || | | ||| | |||| || ||||| || |||||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||| ||||
gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G09160.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------gtatggtgtaatctttatattcctttctaatcaggacttttta----actagcctgttttggttcc-ttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
| ||||| | | || | ||| ||| | | || || |||| || ||| || |||||| || || || || |||||||||||||| || || ||||| || || |||||||| ||||| ||||||||||||||||| || |||||||| |||||||
gtatgatcatttccagtgaatttaagttactgtttcattgtgttttggctgtggtgggtttgtaatgtgtaagaagtccttggattttcaatgatattaatgtgctttgattatgccaatgca---atagGTCGGCCCACTACGATGCTGGCCTGGTGGTTTATGTCTTTCGAGGTCCATTGGTGATACGGATGTGGGAGAATTTATTGTCCCTATACCACACGTTAAGC
upper sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
gtatggtgtaatctttat--attcctttctaatc---aggactttttaactag-------cctgttttggttcctta--------atacat-----ttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
|||| || | | || | || || | | || |||||| | | ||| ||| || | | || || || ||||| || || || |||||||||||||||||||| || || || || |||||||||||||| || ||||||||||| ||||| |||||||||||||||||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctaatcaggactttttaactagcctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
ttaatacatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA