Sequence
atgc intronic sequence ATGC exonic sequence...ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
Basic information
| species | Glycine max |
| transcript | GLYMA06G22900.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g04750.1 (Oryza sativa), 3'ss of exon 1
ctgcccgtgtgttaattttagtttctagggttttatgt---gtatgcctcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
| | || | | | | | || || | | || | ||| | || | | |||||| | ||| ||| ||||||||| ||| | ||||| ||||||||||| || || |||||||||||||| |||||| |||||||| |||||| ||||||| |||||||||||||| |
attttagaatggaacatcaaatattgagtattgaacatcaaatagggctcgctacttgatgtggcaacttcacattgaagactctgttttctgtca---tcagGTCGGTAACCGCATCATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTCCAGCCATCCAGGTGCACCGAGGAGCTCCGCCTGAGGAAAATCAAGAACG
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 3'ss of exon 1
ctgcccgtgtgttaattttagtt-tctagggttttatgtgtatgcctcattga--tttggggatttggtgtttattgaaattaccttttgatgtttcatt--cagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
| ||||| | || ||| | | | | || | | | ||| | ||| | || || | | || | | | |||| | | || |||| || ||| | || || ||||||||||| || || |||||||||||||| |||||| ||||||||||||||||||||||| ||||| |||||||| |
-----catgtgtaatgttcagtcatgtggatatgtagtcttcgggattatttaatttttgaaatcatgtatctgttttactgattgtttgttaatctcttggtagGTTGGGAACCGCATTATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTGCAGCCATCCAGGTGCACTGAGGAGTTCCGCCTGAGGAAGATCAAGAACG
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09690.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttggtgt-ttattgaaattaccttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
| | | || | | | | | | | | | | || | | || |||| || | ||| | | ||||| | |||||||| |||||||||||||||||||| ||||||||||||||||| || ||| || || ||||||||||| || ||||| | |||||||
taatatggattatggattatcctatgacaataacacaaatctttttgctagtactacttatattgggtattatgactgacacatgttgggggtgt-ttcagATTGGCAACAGGATCATAAGGAAGAGGATTCATGTGCGTGTGGAGCATGTGCAGCAATCAAGATGTGCTGAGGAGTTCAAGCTGAGGAAGAAGAAGAATG
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G57860.1 (Arabidopsis thaliana), 3'ss of exon 1
--ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggg-gatttggtgtttattgaaattaccttttgatgtttcattc-agGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
|| |||| | || |||| ||| || | | || | ||||| | | || || || | || || | | ||| || || | || ||||||||||||||||||||||| || ||||||||||||||||| | || ||||| |||||||||| || || || | |||| |
atatgttttgatgttg-tgaaagcttctct--tttcatttct-tgtgtttatgattagtgtaatctgttggagagctaagttggtgtgttgggttgggttttagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAACAGAACG
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttgg--tgtttattgaaattaccttttgatgtt-----tcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
||||| | | | | | | | | | ||| | | || || |||| | | | | ||||| | | ||||| | || ||||| |||||||||||||||||||| || |||||||||||||| || || || || | ||||||||| || ||||| | || || |
-------tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
upper sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G57660.1 (Arabidopsis thaliana), 3'ss of exon 1
ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattc---agGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
| | | | | | | || || |||| | | | || ||| | || | | ||||| | || |||| || || | || ||||||||||||||||||||||| || ||||||||||||||||| | || ||||| |||||||||| || || || | |||| |
-ttgcaatcaatctactatgattcttat--ttttgaaagccttctcttttagtttattgtatttcttggtgggctaattatgtgtttgggtttggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGGAGCATGTGCAACAGTCAAGGTGTGCTGAGGAGTTTAAACTCAGAAAGAAGCAGAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
ttttgat putative branch site (score: 4)
tttcattc CT-rich tract
tgtttattgaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttggtgtttattgaaattaccttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
ctgcccg
- - - - - - - - - - - - - -gggtttt
- - - - - - - - - - - - - - - - - - - gtatgcc
- - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg
