Sequence
atgc intronic sequence ATGC exonic sequence...aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
Basic information
species | Glycine max |
transcript | GLYMA16G23340.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
------------aattgtgtttcaatgct---atatatgat--atcctcttataaatatgct---tattgagaaagaaagata-attttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
||| | || | | |||| |||| || || | | | ||| ||| | || ||| || | | | | | || || |||||| |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaa-cagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------------aattgtgtttcaatgctatatatgatatcctcttataaatatgctt----attgagaaa------gaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
| | || ||| |||| ||| |||| | | || || || | | | | | | || |||| | | || | ||||| |||||||||| || ||||||||||| || || ||||||||||||||||| |||||||||||||| ||||| || ||||||| || || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatga-atcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaa-cagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG
upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
|| ||| |||| ||| | || | || | | ||| | | || ||| | | ||| | || ||||| | | ||||||||||||| || |||||||| |||||||| || ||||| || || |||||| |||||| ||||| ||||| ||||||||||| |
-gttatgtcccaat------tattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgttt---cttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
---aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
|| | || ||| || | || || | || | | || || || || | | | || || ||| || | | | || || ||||| |||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || || ||||| ||||| |
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttcttt-gataggcaaaggacttattgttttatttttgaa--ttattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
upper sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 2
----aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
| || ||| | | ||| || | | | || | || | | |||| || | | | |||| ||||||| || ||||| || || |||||||||||||||||||| || || ||||| ||| || ||||| ||||||||||| || || |
ggcgtactgcaaggagatgtgttgtgcgatgtctcccattcactaaagtctctggtcccttcaacgatttttaaagcacagataattggtcgttttg----cagGATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
ttttttttttcatctc CT-rich tract
agaaagaaagataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
- - - - - caatgct
- - - - - - - - - - - - - - - - - - - -tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa