Sequence
atgc intronic sequence ATGC exonic sequence...ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
Basic information
species | Glycine max |
transcript | GLYMA15G01680.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
----ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
||||| | ||| ||| | | | ||||| | |||| | | | || | | || ||| | | || | | ||| || ||||||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| |||| | |
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttcttattttttaatttatt----ttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
ctattttatttccgtttacagtttttaa--gctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatt-tgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
|| | | | | ||| | | || | | | || || || | |||| | | | || | || | | |||| || || |||||||||||| |||||||||| ||||| |||||||||||| |||||||| ||||| | ||| | |
--ggaaaatgttctatactaatttctgaacgccacttgtgttgctctttataatctcatatcctgagatgt-tctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatatt-ttggaagatatatactaattctccatttcaa-tgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
||| ||| ||| | || |||| | | | || || | || | ||| | | | || ||| || | | |||| || |||||||||||| |||||||||| ||||| |||||||||||| |||||||| ||||| | || | |
atatcctatactggttga--gtccgagtgctgcttgtgttactctttataatttcataatcctaaggtgttctttgttttatactttgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
ctattttatttccgtttacagtttttaa--gctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatt-tgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
|| || | | | ||| | | || | | | || || || || |||| | | | || | || | | |||| || || |||||||||||| |||||||||| ||||| |||||||||||| |||||||| ||||| | ||| | |
ctggaaaatgttctatactgatttctgaacgccacttgtgttgctctttataatctcatcctg--agatgt-tctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------------------------------------------------ctattttatttccgtt----tacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatt--tgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
| | ||| | | || | || ||||| | | ||| || | || | | | || || | | ||| || || | | || |||||||| ||||||||||| || ||||| ||||| ||||||||||| ||||| ||| | || ||||| || ||
gtattataatattaaacagtttttttttgttggacatattatagtaaacgcttcttgtatgccttggctaaaccatctccactttggcttcattcttgtgcactttttca-ccattaccaatttctttt---attgtccttccatttgtaatcccaatttcctaatgtctgttttttcttgcagGCTAGAGAACACATTGAATTATGGCCTTGAGAGAGTCTGGGCAATTGGTTACATTAAAAGTTCACGCCG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
ctattttattt-ccgtttacagtttttaagctgatactaaat--gtagttggaagtat------attttggaaga-----tatatactaattctccattt--caatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
|| | | | | || | || || ||||| || | | | || || || | ||||| || | || | | || | | || | | | | ||||||||||| ||||| |||||||| ||||| || || |||||||||||| || | || |||| || ||
gtaactcgtatgctgtctgca---ttggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 8
---ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
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aaattgtgatgtgtgcctcataagttt---acttatttatttatctattcatctttgcctaatcttaattttaattttgttaaccatgctcagcaatttacagGCTTGAAAACACATTAAATTATGGACTTGAACGAGTTTGGGCCCTGGGATGTATGAGAGGTTCACGACG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
ctattttatttccgtttacagtttttaagctgat-actaaatgtagttggaagtatatt--ttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
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-tgttttttcttaatgtagtgatagatgatagatgattaaacct--ttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGMapped 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|208112800|gb|GD908759.1|GD908759EST: ACTGGTTCTGAGGATGGCACAGTACGCATATGGCACTCCACAACTTATAG GCTTGAGAACACATTAAACTATGGTCTTGAAAG
genomic: ACTGGTTCTGAGGATGGCACAGTACGCATATGGCACTCCACAACTTATAGgtaatgtgaa ... gtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
tactaat putative branch site (score: 1)
aagatatatactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - gctgata
- - - - - - - - - - - - - - - - - - - aatgtag