Sequence
atgc intronic sequence ATGC exonic sequence...tatgcatgcgcttgacttgaggaagtgctgcatcctgcatggctgtgtgcacctgtttgaaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
Basic information
species | Glycine max |
transcript | GLYMA08G22850.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 17
-------tatgcatgcgcttgacttgagg--aagtgctgcatcctgcatggctgtgtgcacc-tgtttg--aaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
||| || | | | || | | |||||||| || | | | |||| |||||| || | | || | | | | |||||||| | | |||| || || |||||||| ||||| | ||||| ||||| |||||||| || ||||||||||| || |||||||| || || |||||| | |||||||| |
gtatttcaatgaatttggtgggctgtattctatctgctgcatagtgatgtgtttttggcacaatgtttggcaactgcatttttcactagacttctgttctttctctgt--agGCAACTATATATCAGCAGAAGGCACTTGATATCAATGAAAGAGAGCTAGGTCTTGACCACCCAGAAACTATGAAGAGTTACGGGGATTTATCTGTCTTCT
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 15
------------------------------------tatgcatgcgcttgac---ttgaggaagtgctgcatcc-tgcatggctgtgtgcacctgt---ttgaaggaaaatatta--attt---atttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
| || | | | || | ||| || || | | | ||| ||| | | |||| | | || || | |||| |||| || |||| || |||| || || |||||||| ||||| | ||||||||||||||||| ||||| || ||||| || |||||||||||||||||||||||||||||||| ||||
gtatcatcatcttttatcttcttcccaaatggaaactttgatttcaagtaacaaatagagagtttgatgttctcgttctaggcactgtatataaataaattgatgagaggtaccgtcatctctgattttttatcctctcttgatc-agGCAACAATATATCAGCAGAAGGCTCTAGATATAAATGAGAGAGAACTTGGTCTCGACCATCCCGACACTATGAAAAGCTATGGGGATCTTTCTGTATTTT
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 17
tatgcatgcgcttgacttgaggaagtgctgcatcctgcatggctgtgtgcacctgtttgaaggaaaatattaattta-tttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
| | || ||||| | | || | | || ||| ||| | ||| | | |||| | | ||| || ||| || | ||||| || || ||||| || ||||| |||||||| |||||||| || |||||||||||||| ||||| || |||||||||||||| |||||||| || ||||
tttccagctgcttggtctc-gttggttttctgtgttgtatgtctgcaagtgactggtccagttgctttattctctaaacttaaattttcttccttgtctagGCAACTATATATCAACAGAAGGCTTTGGATATCAATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTT
upper sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
tatgcatgcgcttgacttgaggaagtgctgcatcctgcatggctgtgtgcacctgtttgaaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
| | | ||| | ||| | || | || | | | ||| || | |||| | | | |||||| || || |||||||| || ||||| ||||||||||| |||||||| |||||||| || || || |||||||||||||| || | |||||||||
-------------------------------gtacacaaaagctacatat---tgtattaatgtaattgatgacttaattgatga-ctttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgcacctgtttgaaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
tattaat putative branch site (score: 2)
tttatttattattctt CT-rich tract
aaggaaaatattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgcatgcgcttgacttgaggaagtgctgcatcctgcatggctgtgtgcacctgtttgaaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT
- -gcatgcg
- - - - - - tgacttg
- - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - gcatggc
- - - - - - - - - - - - - - - - - - - - - - - -tgcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaata