Sequence
atgc intronic sequence ATGC exonic sequence...ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
Basic information
species | Glycine max |
transcript | GLYMA02G17090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5
--ttgttttgcctgggtg-gttaatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaat-tgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
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agccagctccttaagttgtattaatatattagctgtttcctttatgtttgaattttcac---agttgattacatagatcttgatgtgccctgatcttt-tgtagGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6
ttgttttgcctgggtggttaatatgtttgctactcgtacatg-atgaaaattgtcaattaagttgacaattgc----agtctgatgcttatttttccttcta--cagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
| | | || ||| || || || || |||| | | | || |||| || | | ||| | || || || | |||||||||||||||| |||||||| |||||||| || |||||||||||||| | |||||||| || |||||| | | | || |||||| | |
-------taatagatcattgataccttggccttgtatagttgtatgatatagattacttcagttctgaaatctcatgaatctaacatggcttggtcattttggttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCAGTCTTCTAACATGTTGA
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
---ttgttt-tgcctgggtggt-taatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
| || | ||| ||| | || || || ||| | | ||||| || | | | |||| | | |||| | || |||||||||||||||| |||||||| |||||||| || |||||||||||||| | ||||||| || |||||| | || | || |||||| | |
atatcattgataccttggtcttgtatgatattgatcact--tcagttctgaaatttcatgaccagttacacaaatctaac---atgccctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaattgtcaat---taagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
|| | | ||||||||| | | | |||| ||| || ||| |||| || | | ||| | || | ||||||||| ||||||||| ||||| ||||||||||| || ||| ||||||| | |||| |||||| | || || | | | |
----------------gtaattgcttttgctactttgaaaacttaccgtttgtaaatctgtagtgtgaaaattccatcatttttcttttggttttcttcttagGGTTCAACTGTTCCTTTAGTTGTCAAATGGGCAGACACAGAACGAGAAAGACACACAAGAAGACTTCAAAAGGCTCAATCTCACATCGCCCGACTAGGGA
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
----ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaa-ttgtcaattaagt-tgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC-
|| || | || | | | || | || || | |||| ||| ||||||| || || ||| |||||| | | |||| ||| |||||||||| |||||||||||||||| || ||||||||||||| ||||||||| || |||| || || | || || | | |
gtatgtgcttattacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaat----atcacattctt-tttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAG-ACTCGATC
upper sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5
----ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaattg-cagtctgatgcttatttttccttctac-agGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
||| || | || || | ||| || || | ||| | | | || | | || |||| ||||| ||| ||| || | ||||||||||||||||| | ||||| |||||||| ||||||||||||||||||| |||||| | |||||| ||| | || || | | |||||| |||
tccccagttctgtgaagtgggatagtggatttctgccttata-aaaatggaga-----agttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|298170980|gb|HO015956.1|HO015956EST: AACAGGCCTTTACTGCTCTTGAAGCAATCAATGGAAAGCATACAATGGAG GGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAA
genomic: AACAGGCCTTTACTGCTCTTGAAGCAATCAATGGAAAGCATACAATGGAGgttggtgttt ... ccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattgtcaattaagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
gtctgat putative branch site (score: 4)
tgcttatttttccttc CT-rich tract
ttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttttgcctgggtggttaatatgtttgctactcgtacatgatgaaaattgtcaattaagttgacaattgcagtctgatgcttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTTAAATGGGCAGATACTGAAAAGGAAAGACTAGCTCGAAGGGCTCAAAAAACACAGTCCCGAGTTTCTAATGCGCCGC
- -ttttgcc
- - - - - -gggtggt
- - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagtc