Sequence
atgc intronic sequence ATGC exonic sequencegtagtatcttttctctaatcctacatttctttttgtgctcgcatttctgattattccgtggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
-----------------------------------------gtagtatcttttctctaatccta-catttctttttgtgctcgcatttctga--ttattccgtggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
| || | | | | | | ||| | |||| || | || |||| | || | | | |||||| || || || |||| ||||| |||||||| || | || || ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||
gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttt-tgttgctgacctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
-----------------------------------------gtagtatcttttc-tctaatcctacatttctttttgtgctcgcatttctgattat-tccgtggtacttggcatg-cagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
| || | | | | | |||| | |||| || | | || ||||| || | || || | |||||| || || || |||| ||||| |||||||| || | || || ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||
gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgttt-cgttgctgatctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
----gtagtatcttttctctaatcctacat-----ttctttttgtgctcgcatttctgattattccgtggtacttgg-catg-----cagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
| | | | | ||| || || ||| || | ||| | || | ||| ||| |||||| || || || |||||||| || || ||||| ||||| || ||||| || ||||| ||||| ||||| |||||||| || || ||||||||||| ||
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
gtagtatcttttctctaatcctacatttcttt-----ttgtgctcgcat--ttctgattattccg---tggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
|| | ||| ||| | ||||| || | || || || | | ||||| | || || | || | ||| ||||| || ||| | || || ||||| ||||| ||| | || |||||||||||||| ||||| ||||| || ||||| |||||||||| ||||| ||
gt-gaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
gtagtatcttttctctaatcctacatttctttt-tgtgctcgcatttctgattattccgtggtacttggcatg--------cagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
|| | | || | ||| | ||||| || | || || || || | || | || | | || ||| ||||| || ||| | || || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| || ||||| |||||||||| ||||| ||
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
--gtagtatcttttctcta-atcctacat---ttctttttgtgctcgcatttctgattattccgtggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
| || || | | || ||| ||| ||| | | | | | | | | | | | ||| | ||| ||||| || ||||| || || ||||| ||||| |||||||| |||||||||||||| ||||| ||||| || ||||| |||||||||||||| || ||
gtgatgtgtccctaccatatgccctgttcgggttcactttctttttacttcaattgcttatgctttgcatgtggttttcagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAAATCATTATAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctacatttctttttgtgctcgcatttctgattattccgtggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
ttctgat putative branch site (score: 3)
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtatcttttctctaatcctacatttctttttgtgctcgcatttctgattattccgtggtacttggcatgcagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG