Sequence
atgc intronic sequence ATGC exonic sequence...tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
Basic information
species | Glycine max |
transcript | GLYMA08G20830.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctga---tcaaatttggactatggtat-gtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
||| || || | || ||| || | | || || ||| || ||| | || | || ||| | | | | | | | || || || || || | ||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
----ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaataccatgttctcatattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgt--ttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| |||| | | | | | | || | || ||| || || | | | | | | | || || | | | || ||||| || |||||||||||||| |||||||| || |||||||||||||| ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
-tttgctgatgtgcatctcatatacattcgattag-atgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
----tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | | || | || | | ||| | || | | |||| || | | | ||| | ||| | | || || | || ||||| || || || ||||||||||||||||| || |||||||||||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatata---tatattgtaacctctatttccac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctg---aaatctg--atcaaatttggactatggtat-gtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| ||| || | | | |||||||| | | ||| ||| ||| | | | | | || ||| | || | | |||||||| ||||| ||||||||||| |||||| | |||||||| |||||||| | |||||||||||||| || ||||| ||||||||||| || ||||||
-----tgaatgagttaat-gtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgct-----agCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | | || | || | | | | | | | || ||| |||| | || || | || ||| | ||| ||| | | | || ||||| || || || ||||||||||||||||| || |||||||| ||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttgctgatttgcacctcttatatcttaaatgtatg---ctgccat-tttttgtattgtcctattgggtagtga-tatatattatttgtaatctttatttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
tttcatgtatgttttttttgcaccctt-actttttttgtctatcata-cttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| || | | |||| | | | || || || ||| | ||| || || || | | | |||| || ||| | || ||||| || || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | || || || ||||| ||||||||||| |||||| ||
-ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgac-agTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttc--tgaaatctgatcaaatttggactatggtatgtttcaaatatctgcta--gCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | ||| | | ||| | | | | ||| | || || | | | | ||| || | || ||| || || || | || || ||||| || || || ||||||||| | ||| ||||||| ||||| ||||||||||||| || ||||| |||||||||||||| ||||| ||
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
tttcatgtatgttttttt-tgcac-ccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|||| || | | | || |||| | | || || | || | || || |||| | || | | || ||| | |||||| |||||||| || || || ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||
-ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
-------tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
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gaaagactattatggaaacaatgct---aatggtaacttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctc---tctct-ccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCAMapped 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|193511886|gb|FK469995.1|FK469995EST: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG CGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
genomic: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaa ... tatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
EST:
gi|7796415|gb|AW781812.1|AW781812EST: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG CGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
genomic: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaa ... tatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
atctgat putative branch site (score: 4)
tatgtttcaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
- -catgtat
- - - - - - - - - - caccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt