Sequence
atgc intronic sequence ATGC exonic sequencegttttgttttattccctgcattggaagtttttgtgtggtgtagtgttgatgacatttgttgtgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
Basic information
species | Glycine max |
transcript | GLYMA09G04430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 3
gttttgttttattccctgcattggaagttt--ttgtgtggtgtagtgttgatgacatttgttgtgttgat-tggttctttg----tttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
|| | | || | | ||| || | |||| || || | | | | | | || | |||| |||| | ||| ||||| || ||||||||||| || |||||||| |||||||| ||||| |||||||| ||||| || |||||||||||||| || || |||||||| ||||| |
-----gtgtgtgccaacacaatattattttcattatctggta-ggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagTTCGAAGCTGCGTGGGCACTTACAAACATTGCATCTGGCACTTCGGAGAATACAAAGGTTGTCATTGATCATGGGGCTGTACCAATATTTGTGAAGCTTC
upper sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 3
gttttgttttattccctgcattggaagtttttgtgtggtgtagtgttgatgacatttgttgtgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
| | || | || || || | | || | || || | || | | || | | | | || ||| ||||| || || || |||||||||||||| || || ||||| ||||| || ||||| ||||| || |||||||||||||| ||||| |||||||| ||||| |
------gtatgttgatttaatataaaccttatatcctgt-tgttgctggatgaaaatgaatttctcatcagctttgtaattcttttgtagTTCGAAGCAGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGTTGTTATTGATCATGGGGCTGTTCCTATATTTGTGAAGCTTC
upper sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
gttttgt-tttattccctgcattggaagtttttgtgtggt-gtagtgttgatgacatttgttg---------tgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
||| | ||| ||| | | ||||| || | | || | | | || | | || | | | | || ||| |||||||| || || |||||||||||||| || || ||||| ||||| || ||||| |||| || ||||| |||||||| ||||| |||||||| ||||| |
-tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
upper sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 3'ss of exon 3
gttttgttttattccctgc------attggaagtttttgtgtggtgtagt-gttgatgacatttgttgtgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
|||| | || ||| || ||| | || | | || | || ||| | | | || | | || ||| || || |||||||||||| || ||||||||||||||||| || ||||| || || || |||||||||||||| ||||||||||| ||||| || |||||||| |||||||
gtttgggattgttctttgttacattgttgtttggttattagcagttttgtagtttgtttaagtacttatttcaataatggcttcaatt-ttgtctagTTTGAGGCAGCTTGGGCTCTCACAAACATTGCTTCTGGGACATCAGAAAATACCAAGGTGGTAATTGATCATGGAGCAGTGCCAATATTTGTGAAGCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtagtgttgatgacatttgttgtgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
tgttgat putative branch site (score: 4)
ttctttgtttgttt putative PPT
atttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgttttattccctgcattggaagtttttgtgtggtgtagtgttgatgacatttgttgtgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT