Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
Basic information
species | Glycine max |
transcript | GLYMA14G23710.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 4
ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
||| ||| || | || | | | | || || | || || || ||| |||||| ||||||||| || ||| ||||||| || | ||||||||||| | ||||||||||||| ||||||||||| ||||| |||| |||||||| || |
------------------gtatgttacgataatatgccaaagcaatctgtgctgtgaagcccatgataacttttctttaacaacaccaatttat-tgaagGATGATGAAAGAGGCATGCGGTGGTTCTATTCTGGTGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 9
-----ttgt-ttgtt-ttattttatttatt--ttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
|||| ||||| | | | || | || || | | | | | | || |||||| || | | ||| | ||||||| ||| |||| || ||| | ||||| || | |||||||| ||| | | || |||||||| ||||||||||||||||| |||||||||| ||||| |
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
ttgtttgttttattttatttattt-tattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
| | ||| | || || | || ||| | || | | | | ||| | | |||| ||||||||||||||| || ||| | ||||| ||| | || ||||||||| | |||| ||||||||||| |||||||| || || | || ||||| || || |
----------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatatttt-----gaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 9
ttgt-ttgttttattttatttattttattttatgtggagggagg-agagaaggtaaaaaggtacaaattacatgtt---tttactttttac----ttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
|| | || || | || || | | || | | ||| | ||| | || | || | | ||| | || || | | || ||||||| |||||| | || ||| | ||||| || | || ||||| || | | ||||||||||| ||||||||||||||||| |||| || || || || |
--gtatggtgttctcctaccaatatattcatagattgtttcaggcattgaactttaacttcttcacactttctgtaacaataaccacacaccacatatattatgtgaagGATGATGAGAAAGGTATGCGATGGTTCTATTCTGGAGACATCGGACGGTTCCATCCAGATGGCTGCCTTGAAATCATTGACCGTAAGAAAGATATCGTGA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
|| | | ||||| ||| |||| | || | | ||| | | | || ||| ||| || | | || ||||||||||||| ||||||||||||||| ||||| || ||||| || || | || || ||||| ||||| || || || || | |||||||| || ||||
gtggcaaatcaacattattggtttcggca-atgttaaaagaattg-gttggtttggttcttcctctaaccgttttatacacttgaatgttc-----aaagGTTGATGAAAAGGGAATGAGGTGGTTCTACACAGGAGACATAGGACGATTTCACCCTGATGGCTGCCTCGAGATAATAGACCGAAAAAAGGATATCGTTA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------ttgtttgttttattttatttattttattttatgtggagggaggagag-aaggtaaaaaggtacaaattacatgtttttactttt--ta--cttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
|| ||| | | || ||| ||| | | | | | || || || | | || ||| | |||||| | | ||| || ||||| | ||||||||||||| || ||||||||||||||||||||||| ||||| ||| | ||| | ||||| ||||||||||| ||||| ||| ||||||||| ||||
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ26722 (Selaginella moellendorffii), 3'ss of exon 8
ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatg-----tttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
||| || | || || | || || | || | | ||||| ||||||||||| || ||||| ||||| ||||| ||||| ||||||||||| | | ||||| ||||| ||| | ||||| | || | || |||||||||||||
--------------------------------------------------gtacaacttttcagtttccttgaagcgttcatgtttaattcgtttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA
upper sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatg---tttttactttttact---tttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
||| || | || || | || || | || | | ||||| ||||||||||| || ||||| ||||| ||||| ||||| ||||||||||| | ||||| ||||| ||||| ||||| | || | || |||||||||||||
--------------------------------------------------gtacaacttttcagtttccttgaagcgttcatgcttaattgggtttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
tgtttttactttttac CT-rich tract
aaattacatgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttgttttattttatttattttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-tgtttgt
- - - - - - - - - - - - - - - - -tggaggg
- - - - - - - - - - - - - - - - - - - - - - - - -ggtaaaaa