Sequence
atgc intronic sequence ATGC exonic sequence...atttatatttacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
Basic information
species | Glycine max |
transcript | GLYMA09G33240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.2 (Arabidopsis thaliana), 3'ss of exon 3
-atttatatt-tacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| | | | ||||| || | | || | | | | || | | | ||| | ||| | | | || | | |||||||||||||| || ||||| ||||| ||| || |||| ||||| ||||||||||| |||||| | | |||||||||||||| ||||||
aatcaacagtatacttgggtaagaacaaatatcttaatc-agtcagcatgtgaataatgttgaatatgtatctgtggtgtc-taactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.1 (Arabidopsis thaliana), 3'ss of exon 4
atttatatttacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
| | | || || | || ||| | | | || |||| | ||| | ||| | | | || | | |||||||||||||| || ||||| ||||| ||| || |||| ||||| ||||||||||| |||||| | | |||||||||||||| ||||||
-----------gtaagaacaaatatcttaatcagtc----agcatgtgaata-atgttga-atatgtatctgtggtgtc-taactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 4
atttatatttacttcaaga-atgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|||| || | | | | || || | || ||| | | | || |||| | ||| | ||| | | | || | | |||||||||||||| || ||||| ||||| ||| || |||| ||||| ||||||||||| |||||| | | |||||||||||||| ||||||
--gtatacttgggtaagaacaaatatcttaatcagtc----agcatgtgaata-atgttga-atatgtatctgtggtgtc-taactttgttaatgattcagGTGGATATGACAAAGAAGATAAGGCAGCTCGAGCTTACGATTTAGCAGCTCTGAAATACTGGAATGCTACTGCTACCACCAATTTCCCT
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 4
atttatatttacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
||| | | | | | |||| || | || | ||| ||| | | | | ||| | || | |||||||||||| |||||||| | || |||||| | ||||| ||||||||| | || ||||||||| | |||||||| || || || ||
-------------gtaagcaagataat-attctattgacaaattaattgatatatc----gagtatggcaaatgatgtccatctttgattaattca--agGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 3
atttatatttacttcaagaatgctcctcaacctatcct--aaagcttttttctgtattttgagagatggttttgtaa--catagtgaa-ttgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
|| |||| | || ||| ||||| || || || | | | | ||| || | | || || | |||| | ||||||||||| ||||| |||||||||||||| || || | |||||||| |||||||| |||||||||||| | |||| || ||||| ||||||
-----cgttcgcttcctttgttctttctaacaaatcctctaatactgggttgaacagtattacagagtattaaattaattatgatggacttgtgtaaattatcagGTGGGTATGACAAGGAAGAAAAGGCAGCAAGGGCCTATGATTTAGCAGCTCTAAAGTACTGGGGTGCTTCTGCAACTACCAATTTCCCT
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------atttatatttacttcaagaatgctcctcaacctatcctaaagctttttt---ctgtattttgaga---gatggttttg--taacatagtgaattgtcttgttta-tcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
| ||| | | | | | | | ||| || | | | | || | || ||| |||| | | | || || || | ||| ||||||||||| ||||||||||| || ||| | || || |||||||| || || ||||||||||||| | |||| |||||| ||
gtatgactggagggacttgaagcacagaaccctctccatgtgcttccttctgagccgttgtgaagttcaaagaacagtctgctgaaagtttgagctagaacagtcattggatgatcaggcgatgattgctatgtggtgaaggttgtatacgcagcatctcacgatctaatgtgtttgggcactgtcacgtgctgcgcagTATACTTAGGAGGATATGATAAAGAAGAAAAGGCAGCCAGAGCCTACGACTTGGCAGCGCTCAAATACTGGGGTCCCAGCACCACCATCAACTTTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
ttgtaac putative branch site (score: 2)
tcttgttt putative PPT
tgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttatatttacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - -gaatgct
- - - - - - - - - - - - -ctcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtt