Sequence
atgc intronic sequence ATGC exonic sequencegtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
Basic information
species | Glycine max |
transcript | GLYMA04G03710.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
| | | || |||| | | | || || | | | | |||||| || ||| | || ||| || ||| | || || | | ||||| || ||||||||| |||||||||| |||||||||||||| || ||||| || | |||
------gtaaatttagtctagtaattgcagattatttaactttaa-----ccggatcattt-ttctcaacataattccttttgcttt-cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
||| | | ||||| || || || | | |||| ||| | | ||| | || || | || | | ||||||| | || ||| |||| ||||| || |||||||||||| ||||||| ||||| |||||||| || ||| || | |||||||||
gtactacttttataaaattcc--atcgtaccaatatgaagt-ctagtgact--aattctgaatatttatc---accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 11
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
||| | | ||||| || | ||| || | | |||| ||| |||| ||| | || || | || | | ||||||| | || ||| |||| ||||| || |||||||||||| ||||||| ||||| |||||||| || ||| || | |||||||||
gtactaattttataaaattct--attccaa---tatgaagt-ctagtgattataattctgaatatttatc---accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTTTGCAACATTTAAAG
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
-------gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
||| | ||||| | |||| | | | || | ||| | | ||||| || | | ||| ||||||||| ||||||||||| |||||||| ||||||||| | |||| || |||||||| ||||| |||||||| | || ||||||
gtattcccctatcttcatgttgttttattcttgataattatcttga-catttggggctaggaattctaatttttgctg-gatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S31_198V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------------gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattaga--atcattcattttcactttg-gttgcttactctaa-----------acagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
| ||| || | | | |||| ||| | | | ||| | || || | | | | || | | || | | |||| |||||||||| ||| |||| ||||||||||||||||| | || || | || ||||| || | | ||||||| |||
gtttaactctacagcacaatcaccgtttataagcattttcagtaactggtaggaaatttgaaatcctgatgctattatggagaagtccataacttaactgcagagtataacgaatatgccagtgatggatgatacagAGGGGACAGTTAAAACGGCCGGATCATGCTGATTTGAGATTTAAATGTCGAACTTATGCTCGAATGTTACAGCATTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
tgcttac putative branch site (score: 2)
cttactct CT-rich tract
ttagaaattagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC