Sequence
atgc intronic sequence ATGC exonic sequence...tcataaactgtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA19G04210.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
----------tcataaactgta-----tgagcaacatattcttattttcaccataaataa---catgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaac--agATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
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gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------tcataaactgtatgagcaacatattcttattttcaccataaataacatgt---atttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
|| | ||| || |||| || || || || || | || | | || | | | | || | | | | ||||||||| | ||||| |||||||| ||| |||| ||||||| |||||||||||||| || ||||| ||||| ||| |||||| | | ||||||||
gtaagtcaatctggaaccatccttttttgataaaaaaaaatgcatgtgtatgtgtgtgtatatatacttctgacctatgtctagattcgtagccaaaatttattttttttaaggacagaaggtgtatataccatctctctatcttttgctcacgaagttttttttttctccttgtatgttagATGATACTACGATGCTATGGGGAGTAAAGCCCTACTATGATTTGCTCATGCAAGCTGGTCCGCTTGGAAATGTGCAAGGAGAACTGATTGTGAGAAAGGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
tcataaactgtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttt-----taacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
| || || ||| | || | ||| || | || | | | || | |||| || || | | |||||||||| |||||| | ||||| || ||||||||||||||||| || |||||||| ||| ||||| ||||| ||||||||||| || || | |||||
---------------gtaa-gtaaacttgtctt-atagaaaagaatagaaataaaccaacctacctcccaacctctcctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 5
tcataaactgtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
| || || | | || | | ||| |||| || | | | ||| | ||| |||| | || |||||||||| |||||| | ||||| || || |||||||||||| | || |||||||| ||| ||||| ||||| |||||||| || || || | |||||
-----------gtaagtaaact--tgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatg-taatttatctgtcccattt----cagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 5
tcataaactgtatgagcaa-catattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
| || || | | | || ||| ||| | || |||| | || || | | | || ||||| | | | ||||||||| | || || |||||| | ||||||||||||||| | | ||||||||||| || |||||||||||||||| || ||||| ||| || ||
gtaagtacaccatcatctatcagtcccttgtttctatagaaaggaacaaatctt------gatgtgttttttttgtttttgatttgat---------atagATGATACTGGGATTCTCTGGGGAATAAAGTTCTACAATGATCTGTTGATGCAAGCTGGGCCATTTGGTAATGTACAATCTGAGCTACTTTTCCAGAAAGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 5
---tcataaact-gtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
|||| | | |||| ||| || | | | ||| | | | ||| | ||| | | || || | | || | |||||||||||| || ||||| ||||| |||||||||||||||||| | ||| ||||||||||||||||||| |||||||| ||||| ||||| || | |||||
atatcatcgctttgcatga-caaaatgtgcatgtttccctttttggtt-tatgacatattgaaaattgaacatgggtataacaagttct--tttttcccaacagATGATACTGCCATGCTATGGGGGGTTAAGTTCTACAATGATCTGCTCGTGCAAGCTGGCCCTCTTGGAAATGTACAGTCAGAGCTACTCTTTCGGAAGGA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 5
---------------tcataaactgtatgagcaa------catattcttattttcaccataaataacatgta--tttttgtagaggcgccaaaatgattattgatctaagttactttta-acagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
||| | || | |||| | | | ||| ||||| |||||| | | || || | || || || | || | | || ||| |||||||| || || ||| | |||||||| ||||| ||||||||||| ||| |||||||| |||||||| ||||| || ||||| |||||||| |||||||
gtacgtcatatcttctcaagatttggttttgcaaagttgttgtctgccagctttttaaataaaaaacatgcaactgttcgtcttaatcctaacatc-ttgtgaatatgaattttggttatacagATGACACTGCCATGTTATGGGGAGTCAAGTTTTACAATGATTTGCTCTCTCAAGCTGGTCCTCTTGGGAATGTGCAGTCAGAGCTACTATTTCGAAAGGAMapped 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|151404928|gb|EV274742.1|EV274742EST: CCAACTTTTCAGTTTCAACTACAAATCAATTACTCCCTACGGATCAATAA ATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGC
genomic: CCAACTTTTCAGTTTCAACTACAAATCAATTACTCCCTACGGATCAATAAgtaagtgtgg ... cttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
tattgat putative branch site (score: 3)
ttactttt putative PPT
aaaatgattattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcataaactgtatgagcaacatattcttattttcaccataaataacatgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaacagATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - tgtatga
- - - - - - - - - - - - - - - - tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccaaaa