Sequence
atgc intronic sequence ATGC exonic sequencegtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgttctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
Basic information
species | Glycine max |
transcript | GLYMA20G30860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0072g00240.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgtt------ttctttgttctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
|| || || ||| | | || ||| | || | | | || | | || | | || | | || || | | | | | | || | | | | || |||||||| | || ||||||| ||||||||||||| ||||||| ||||| |||| ||||| ||||| || || | |||||||| || || ||||||||||||||||
gtatgctgttcagtttacaatttatggtagttgtttc-tatttgttcttgttccattccttctgtctggagctgttttgtgttcccttctatttgggaaatgttatatacaaattcatctaacttcttgtttttatgtgcagCGCAATTACCGTTTCTTCTTTATGTTTGTTTCTTCTTCAACTCTTCTTTGCATATATGTCTTCGCCATGTCAGCTTTCTATATTAAGGTTCTGATGGATA
upper sequence: GLYMA20G30860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ05613 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgtt-ctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
||| ||| |||| || || | || || | | || ||| |||||||||||||||||| |||||||||||| | || | ||||| | ||||| ||||||||||| | | | | | ||||||||| |||||||
--------------------------------------------------------------gtaagct--ccacttcttcctgttatcacttacagaccagctttccacttct--cttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTTGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGTACCGTCTACATCAAGTCCGTGATGGACG
upper sequence: GLYMA20G30860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ28891 (Selaginella moellendorffii), 3'ss of exon 3
gtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgtt-ctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
||| ||| ||||| || || | || || | | || ||| |||||||||||||||||| |||||||||||| | || || ||||| | ||||| ||||||||||| | | | | | ||||||||| |||||||
--------------------------------------------------------------gtaagct--ctacttcttcctgttatcacttacagaccagctttccccttct--cttgcagAGGAACTACCGTTTCTTCTTTATGTTCGTGTCGTCGGCAACGCTCTTGTGCGTCTATGTGTTTGCGATGTGCACCGTCTACATCAAGTCCGTGATGGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttacttgttttctttgttctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
ttctcac putative branch site (score: 2)
tttttgtgccttttcc putative PPT
tatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgttctcacgtatttttgtgccttttccaatgtgcagAGGAACTACCGTTACTTCTTTATGTTTATTTCTTCAGCAACTATTCTGTGCATCTATGTGTTTTCCCTCTCAGCTTTTTACATCAAGGTTCTGATGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA