Sequence
atgc intronic sequence ATGC exonic sequence...tctgtgttttatataacaactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
Basic information
species | Glycine max |
transcript | GLYMA09G33920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
--tctgtgttttatataacaactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatac-agGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
| | | | | | | | | | | || | | | | || || | || | ||||| ||| || | | | ||| |||| || || |||||||||||||| | |||||||||||||||||||||||| |||| || ||||| || |||| | || ||| | ||| | |||||
ccttaatttgatttgcactcagctgacaatcgggagagattattttctcag-ctaacaattatattgcgccctaacgatctca--tcggtgccttcttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
---tctgtgttttatataacaactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
| || | | | | | || | | || | | | | ||| | || | ||||| |||| | | ||| ||||| || || |||||||||||||| | |||||||||||||||||||||||| |||| || || ||||| |||| | || ||| | ||| | |||||
tcacatatgatctgcactctactggcaattggaagatgct--attttctcagcaaacaatttatattgcaccctaacgatgtcatctgtgcctttttac-cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------tctgtgttttatataacaactc-------aagctgtg-tgccttttcatatgccctgtcttttttttctcttcc----tttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
| || ||| | ||| | | | || | | || ||| | || || | | | | ||| || || || | | | ||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| || || |||||||| || | | | || |||| | ||||| |||
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
upper sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
tctgtgttttatata-acaactcaagctgtgtgccttttcatatgccct--gtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
|| || || | || || ||||||| | | | | | | ||||| | || || | ||| | | || || | ||||||||||||||||||||||| |||||| | ||||||||||| ||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||||
---gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
upper sequence: GLYMA09G33920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g01810.t01 (Vitis vinifera), 3'ss of exon 1
-tctgtgttttatataac--aactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
| | | || ||| ||| || || ||| | | | ||| | |||| || | | | || | ||| | ||| | || | |||||| |||||||||||||||||||| || |||||||||||||||||||| ||||||||||||||||| ||| | | |||||||||| | ||||||||||
ttttattttgtatgtaatcaaagtctctttgtattctgctgattatagtttccctttcttccccatcctattttcctatcttg---tcactgtctgcaaacagGGATTCAGGAAGGTTGATCCAGACCGTTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAACACCTATTGAGGAGTATAAATCGGCGAAAACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
ttctaac putative branch site (score: 1)
aattcattatcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgtgttttatataacaactcaagctgtgtgccttttcatatgccctgtcttttttttctcttcctttctaacatcgtcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAGGGGTCAAAAGCACTTGCTTAGGAGTATAACAAGACGAAAACCTG
-ctgtgtt
- - - - - - - - caactca
- - - - - - - - - - - - - tgtgtgc