Sequence
atgc intronic sequence ATGC exonic sequence...ctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
Basic information
species | Glycine max |
transcript | GLYMA08G34280.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G34280.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 6
-ctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
| | || | || || || | | | || | | | | || | | | || | | | |||||| ||||||| ||| | ||||| ||| || | || || ||||| ||||||||||||||||||| || ||||||||||||| |||||| | || ||
gtgagttagcgtcccatcatacttcattcgttctttctcaaacggtctttgctacctttgcttattgtaggaacataattgagagatgatttta--tgcagGGCAATACTACAGGCGGCACTGATGGTGATGCTAAACAATCTGAAGTGAAGGAAAAATTGCCCATCAAAAGATCAAGAGGAAGCTTGGGAAGTTTGAACA
upper sequence: GLYMA08G34280.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 3'ss of exon 6
ctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
| | | | | | ||||| | | | || | || | |||| | ||| | |||| || ||||| ||| | | | || || | || ||||||||| |||| | |||||||||||| || |||||||||||||||||||| | || |||
---------gtgagttttctctgttatcactgtttttattagagtatgggtcagatgggatcttgcttgaagaat------------gttttggattcagGGTAATACTGGAAGTGTTATTGAGGGTGATGGTAAACCATCTGATGGGAAGGAAAAATTGCCAATCAAAAGATCAAAAGGAAGCTTGGGAAGTTTGAATA
upper sequence: GLYMA08G34280.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 3'ss of exon 6
ctgtctcttgcttgctcttttttaca--tcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
|| || || || | || | ||| | | | |||| | | | | ||| ||| || |||| | || ||| |||| |||||| | || || |||| |||| || ||||||| | |||| | ||||||||||| || ||||||||||||||||||||| | || |||
--gtgagttaattaagctactgtatcatttggtctgctgctgagtagacatattctttttcatatggatct--gtagaa-taacttgtaaattttcatgtagGGAACCACTCCGGGAAGCATGGAAGCTGATGGTAAATCATCTGAGGGTAAGGAAAAATTGCCCATCAAAAGATCAAAAGGAAGTTTGGGCAGTTTGAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
aagtaac putative branch site (score: 2)
tacaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
ctgtctc
- - - - -gcttgct
- - - - - - - - - - - - - tcaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctaca