Sequence
atgc intronic sequence ATGC exonic sequencegtatatttctgttgaatttctaattataaactataaatggatcaacctttgttatccaatttttttacgattcttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
Basic information
species | Glycine max |
transcript | GLYMA18G47590.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 9
gtatatttctgttgaatttctaattataaactataaatggatcaacctttgttatccaatttttttacgattcttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
| |||| || | | | || || | || | | | ||||| || | ||| | | | | | | | |||| || ||| | | || ||||| ||||| ||||||||||||||||| |||| ||| || ||||||||| ||||||||||||||| ||||||| | |
-----gtaatgttcaagtcatgaatagaacccattattcccccggttcttgttt----atatgcttatcggttggttactctgtca-----atagTTGCTCCCTGTGCTGGCATCTGCTCTTGAGTTTGGTTCAGCTGCTGCACCAGCCTTGGTTGTATTGTTGAAGATGGGTTCCTGGCTTCCAGCTGACCAAT
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 9
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 9
----------------------------------------gtatatttctgttgaatttctaattataaactataaatggatcaacc---tttgttatccaatttttttacgattcttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
|| || | | | | | |||| | ||| || | || | | |||| | ||| | | || || | | | ||||| | || ||| |||| |||||| | |||||||||||||||||||| || |||| || |||| ||||| || ||||||||||||||| | ||||| | |
gtacttccaaagtgtcaagtagaaccctctattccctcgttcatgattattctctacctttgtttattcgtttcaaaccagccaggtgagtaggtgaccttatttgtatacttattatttgggttactttgtgcacagCTGCTCCCTGTATTGGCTTCTTCTCTTGAATTTGGTTCAGCTGCCGCTCCAGCCTTAACTGTTTTGTTAAAGATGGGTTCCTGGCTTCCTGCTGACCAAT
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatatttctgttgaatttctaattataaactataa--atggatcaacctttgttatccaattttt---ttacgattcttatgttt-----ttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
|||| || ||||||| ||| |||| | | | | | |||| | | |||| || | || || ||| ||| || ||| | |||||||||||||||||| ||||||||||||||||||||||||| | || || ||||| || | || |||||||| ||| | ||| |||| || |
gtatgaatc---tgaatttt--attgggtactaggataacaatttaccttttgagttggaggttttgtgttttgctttttgactttaaccttttggttaatgcagCTTCTTCCTTTATTAGCTTCTTCCCTTGAATTTGGTTCAGCTGCTGCTCCTGCATTAACTGCCTTACTTAAGATGGGTTCGTGGTTATCAACTGAAGATT
upper sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 9
gtatatttctgttgaatttctaattataaac--tataaatggatcaacctttgttatccaatttttttacgattc--ttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
| | || |||| ||||| || ||| | | | | || | | | | | | | | || ||| |||| | |||||||||||||||| | || || || || | |||||||||||||||||||| | || ||||||||| | |||||||||| ||| |||||||||||||| || |
--gtgtgactattga-tttctgatgtgaaatgtcacacttagttctaacagcaatgtttttccatgccaagttctgattttgtcattttctattcacagTTACTTCCTATGTTGGCCTCCGCTTTAGAATTTGGTTCAGCTGCTGCTCCTGCCTTGACTGCACTATTGAAAATGGCTTCTTGGCTTTCAGCTGAAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaacctttgttatccaatttttttacgattcttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
ttcttatgttttttta CT-rich tract
aatttttttacgattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttctgttgaatttctaattataaactataaatggatcaacctttgttatccaatttttttacgattcttatgtttttttattttcacagTTACTTCCTTTATTAGCTTCTGCCCTTGAATTTGGTTCAGCTGCTGCCTCAGCTTTGACTGCATTGTTGAAAATGGGTTCCTGGCTTTCAGCTGAGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG