Sequence
atgc intronic sequence ATGC exonic sequence...gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
Basic information
species | Glycine max |
transcript | GLYMA11G01670.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
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-------gtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaaattat---------------acccaattt--agGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 8
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactg--tattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
| | | | || | || || | ||| | ||| || | | | | || || || ||| | | || | | | || ||| ||||||||| |||||||| ||||| |||||||| | |||||||||||||| |||||||||| ||||| ||||| || || |||| | |||| ||||
-ccagaactggtaatcttcatgaaatttgaattgtggttcaagcaattatgatctattattcttttttttttttttta-attttataatctatttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGAGAGGATCATCCAGAGGAACTAATATCTTTCCTTAGTAAAATGCCCAATG
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ15850 (Selaginella moellendorffii), 3'ss of exon 6
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
| || | || || | ||| ||||| | || | | | ||| | || ||| |||| ||| | ||||||||||| || ||| || | |||||||| |||| ||| |||||||||||||| |||||||| | | | | |||| |
-------------------------------gtaatgctgttcttagttttttgttcttgcttttgttttaagttctttctccttttc--ctttttccagGCATGGATCCTGGATGCAACACCGGGAGAAATACGAGCAGGCGGAGGTGGTGAAGATCATCCAGCGGAACTCATTGAAGCCTTGCGAAGATTGCCTGCTC
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32975 (Selaginella moellendorffii), 3'ss of exon 6
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
| |||| || || | ||| ||||| | || | | | ||| | || ||| |||| ||| | ||||||||||| || ||| |||| |||||| | |||| ||| |||||||||||||| |||||||| | | | | |||| |
-------------------------------gtaatgttgttcttagttttttgttcttgcttttgttttaagttctttctccttttc--ctttttccagGCATGGATCCTGGATGCAACACCGGGAGAAGTACGAGCACGCGGAGGTGGTGAAGATCATCCAGCGGAACTCATTGAAGCCTTGCGAAGATTGCCTGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
tcttaat putative branch site (score: 3)
ttaattgtttcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- tgacaag
- - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - cactgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttct