Sequence
atgc intronic sequence ATGC exonic sequence...tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
Basic information
species | Glycine max |
transcript | GLYMA15G23150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g52340.1 (Oryza sativa), 3'ss of exon 2
-tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctca-tgtttcttctgtgctaaagactagtgggtgaaattttttat--agGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
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gactattttatt--tgttaactttgtgtatgattgcaccaaaata--tgacattgaaaataaacactcaaaaaaattcacttgtttatttgctttcttgtttagGTTAAATTGTGGTGTGACTGCCCTTTCTGGCCTGATGATGGAATGTGTCGGCTTAGGGATTGTAGTGTCTGTGAGTGCCCAGAGAATGAGTTTCCTGAGC
upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 2
------tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttata-gGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
|||||| | | |||| | ||| | | | | | | | |||| | | || | || | |||| || ||| || || ||||||||||||||||| ||||| |||||||| ||||| | | | || |||||||| ||||| ||| | || ||||| |||||||||
tgtgatgccaccaaaatactcaca-ttaaaaataaaaaatttctgcagtggccag---tggctcatctgttctaagtcacgtgctgttccttg---tcttttgtaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGCTCAGAGAATGAGTTCCCCGAAC
upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
-tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagacta-gtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
||| | ||||| || | |||||| | | || | | | ||| ||| ||||| |||| | || | | | ||| |||| || || ||||||||||||||||| ||||| |||||||| ||||| | | | || |||||||| ||||| || || || ||||| ||||| |||
ctatatgtgaatatgactaccaaaatgc--tcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtcttttaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 2
tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
| | | ||||||| || | || | | || ||| ||| | ||| |||||| || | |||||||| ||||| || |||||||||||||||||||| ||||| | ||||| ||||| |||||||| ||||||| || ||||| |||
--------------gttggtt---catatttcttctttgatcatgaaagtatctagaggatttggaggtgtgttgtgataggtttgaatgcgtttaatagGTTAAACTGTGGTGTGATTGCCCGTTTTGGCCTGATGATGGCATGTGCCGGTTAAGAGACTGCAGTGTTTGTGAATGTCCTGAAAGCGAGTTCCCTGAAG
upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 2
tatgttggaatactgataactaaat--gcatttctttttcacttttg-ttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
|||| | ||| | ||| ||| ||||| ||| || ||||| | || | | | | || ||| || || | | | | |||| ||||| |||||||||||||||||||||| |||||||| ||||| | |||||||| || ||||| ||||||||||| |||||||| ||||| |||
-ttgtttattctgttatacttcaattgatattgtgttttcgcttatgcttgactgacctatatcccatttt--ctgaagcctgttgatccatttctatggtagGCTAAGTTGTGGTGTGACTGCCCTTTCTGGCTAGATGATGGTATGTGCCACTTGCGGGATTGCAGTGTTTGTGAATGCCCCGAAAATGAGTTCCCTGAAAMapped 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|13477810|gb|BG507539.1|BG507539EST: ACCCTTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAG GTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGG
genomic: ACCCTTCCCTCCAGGAGCTCGTGAAGACCCCTTTCTTTCGATATTTTAAGgtttgcttat ... ttttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
tgctaaa putative branch site (score: 2)
ttttttat putative PPT
tgaaattttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgttggaatactgataactaaatgcatttctttttcacttttgttgaccctctcatgtttcttctgtgctaaagactagtgggtgaaattttttatagGTGAAGTTATGGTGTGACTGCCCTTTCTGGCCTGATGATGGCATGTGTCGGTTGCGGGACTGTAGTGTGTGTGAATGCCCTGAAAATGAATTCCCCGAAT
-atgttgg
- - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggtg