Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatataccaactctcacattaccatgttttctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
Basic information
species | Glycine max |
transcript | GLYMA10G02130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G02290.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------gtatgcatataccaactctcacattaccatgttttctggtttttgtttttggt---ttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
| | | | ||| ||| |||| |||||||| | ||| | || |||| ||||| | || |||| ||||| |||||||||||||||||||| || |||||| | ||||||||||| || ||||| ||||| ||||| |||||||||||||| || ||||| |
ttaaattctgtatcaatatcgtcaaaagatcaaatctt-tattagt-tgttttctttcccctctttccaaaaaatctctaatttgtgtgt---tttgttgattagGTGGATTTGGTTGGAGGGTACTATGATGCAGGAGACAATATCAAATTTGGTTTCCCAATGGCATTCACAACCACAATGCTTTCATGGAGTGTAATTGAAT
upper sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
----------gtatgcatataccaactctcacattacc------atgttttctggtttttgtttttggttt-gcttatttatgtgtgaatgtgcaa-tgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
| || || | ||| ||||| | |||| ||||| ||||||| | | |||| | ||| | || || ||||||| ||||| ||||||||||||||||| || ||||||||||| || ||||| || || |||||||||||||||||||||||||||||||| || || ||||
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttgttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT
upper sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcatataccaactctcacattaccatgtttt--ctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTT-GGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
| || | | | | || ||||| | | | ||| | | | || ||| | | || | || || ||||| ||| || |||| ||||| ||||| ||||| || |||||||| ||||| | ||||||||||||||||||||| || || |
----------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatc-tctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
upper sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcatataccaactctcacattaccatgttttctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
|||||| | | | || | | | ||| | | | ||| | | || || | | | ||| ||| | | | ||||| ||| || |||| ||||| ||||| ||||| || |||||||| ||||| | ||||||||||||||||||||| || || |
gtatgcgtttctgagatcctgc----tcgt-tttataagaagctctacttgatctctttggttgttc-----tcttcaa----gGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
tttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatataccaactctcacattaccatgttttctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA