Sequence
atgc intronic sequence ATGC exonic sequencegtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttgaaagcaattgctccccttgttatttaattatttatgtctaatgtcgagattatgttgctaacctgcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
Basic information
species | Glycine max |
transcript | GLYMA09G37610.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 18
gtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttgaaagcaattgctccccttgttatttaattatttatgtctaatgtcgagattatgttgctaacctgcataatctgtca-aaaatagc--atcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
|| | | || | | | | ||||| |||| | || ||| | || | ||||| | | | | || || | ||| | || |||||||| ||||| || ||||||||||| |||||||| | |||||||| |||||||| || |||
-------------------------------------------------------------------------------------------gatcgtctgcaacttgtctt-atagtatgtggctatgcgttattttctcttgtaatgttatttatcatctgagtatatgttcatgat-ggtgtac-ttgtcagATGTCAGCAGCAGCATTTGCCAAAGGCCTTCTTGATTTGGAAGGGCAACTAACACCTATACTG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttga-aagcaattgctccccttgttatttaattatttatgtctaatgtcgagattat--gttgctaacctgcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
| | | || | ||| || || |||| || | | || || || || || | | | | | || | | || ||| ||| ||| | |||| || || | | || | | ||||| ||||||||||||||| |||||||| ||||| || |||||||| ||||| ||||| || |||||||||
--------------------------------------gtacagatttacgcttttagtagtgaagatgagcatatgatattca-attgttgaac-atatactgcaagctttactactcctcactgtttgcac-caaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 19
gtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttgaaagcaattgctccccttgttatttaattatttatgtctaatgtcgag-attatgttgctaacctgcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
| | || || |||| | | | | ||| ||| || | || | || |||| | | |||| || || | |||| | ||| |||||||||||||| |||||||||||||| || |||||||| ||||| ||||| || |||||||||
------------------------------------------------------------------------gtacaactttctgccgatttcgtattgacgatgaccattgagcattcaaatgttcac-tatatcttctgg-atattcctcatcggtt----gcactgagatatgatatgaatgtatgcagATGTCTGCAGCTGCTTTTGCCAAAGGCCTGCTTGACCTAGAAGGACAGCTGACCCCAATCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
atttaat putative branch site (score: 4)
tctctgtt putative PPT
aaaaatagcatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttgaaagcaattgctccccttgttatttaattatttatgtctaatgtcgagattatgttgctaacctgcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT