Sequence
atgc intronic sequence ATGC exonic sequencegtttgttctttagccttctgctttttttttcccctgctctgctctctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
Basic information
species | Glycine max |
transcript | GLYMA08G34280.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgttctttagccttctgctttttttttcccctgctctgctctctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
|| | || || | ||| | || | ||| | || ||| || | | || |||||| | || | | || | |||||| ||||||| ||| | ||||| ||| || | || || ||||| ||||||||||||||||||| || ||||||||||||| |||||| | || ||
---------------------------------gtgagttagcgtcc-catcatacttcattcgttctttctcaaacggtctttgctacct----ttgcttattgtaggaacataattgagag------atgatttta--tgcagGGCAATACTACAGGCGGCACTGATGGTGATGCTAAACAATCTGAAGTGAAGGAAAAATTGCCCATCAAAAGATCAAGAGGAAGCTTGGGAAGTTTGAACA
upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgttctttagccttctgctttttttttcccctgctctgctctctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
| | | | | | ||||| | | | || | || | |||| | ||| | |||| || ||||| ||| | | | || || | || ||||||||| |||| | |||||||||||| || |||||||||||||||||||| | || |||
------------------------------------------------------gtgagttttctctgttatcactgtttttattagagtatgggtcagatgggatcttgcttgaagaatg------------ttttggattcagGGTAATACTGGAAGTGTTATTGAGGGTGATGGTAAACCATCTGATGGGAAGGAAAAATTGCCAATCAAAAGATCAAAAGGAAGCTTGGGAAGTTTGAATA
upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 3'ss of exon 6
gtttgttctttagccttctgctttttttttcccctgctctgctctctgtctcttgcttgctcttttttaca--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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttctttagccttctgctttttttttcccctgctctgctctctgtctcttgcttgctcttttttacatcaccctgtattttctccttcctgttctgtattgtctttatccaagtaaaagtaacctacaattttacatgcagGGAAATGCCCCAGGCCGCATCGAAGTTGGTGGTAAACCTCCTGAAGTGAAGGAAAAATTACCTATCAAAAGATCAAAAGGAAGTGCTAGTGGTGGTAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG