Sequence
atgc intronic sequence ATGC exonic sequence...ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctga---tcaaatttggactatggtat-gtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
||| || || | || || || | | || | | | ||| || ||| | || | || ||| | | | | | | | || || || || || | ||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
---ctgtgtgagttctctgaacctataatactacctgcttct-gtatattttcaaatcatgagcatgaagctaataccatgttctcatattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgt--ttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| ||| | | | | || ||| | | | || || | | | | | | | || || | | | || ||||| || |||||||||||||| |||||||| || |||||||||||||| ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
tttgctgatgtgcatctcatatacattcgattagatgt--aatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtat-gtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| ||| | || | | || |||| | | | ||| |||| | | | | | | || ||| | || | | |||||||||||||| ||||||||||| |||||| | |||||||| |||||||| | |||||||||||||| || ||||| ||||||||||| || ||||||
tgaatgagttaatgtggc-tgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttgg-actatggtatgt-ttcaaatatctgct-----agCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | | | ||||| || | |||| | | | |||| | || | | ||| || | || ||| | || || ||| | || ||||| || || || ||||||||||||||||| || |||||||||||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
----tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgcc---atttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
-ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatca-aatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | | |||| | || | | | | | || | | | | || | || | | || | | ||| | | | || || | || ||||| || || || ||||||||||||||||| || |||||||| ||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
ttgctgatttgcacctcttatatcttaaatgtatgctgccattttttgtattgtcctattgggtagtgatatatattatt-tgtaatctttatttcaac-agTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatg-cttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| || | ||| | | || || || || | ||| || || || | | | |||| || ||| | || ||||| || || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | || || || ||||| ||||||||||| |||||| ||
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgac-agTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
ttcatgtatgcattttttgcgcccttatttttgtttg-tctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgcta--gCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | | || | ||| || | | | | || | | || | | | | ||| || | || ||| || || || | || |||||||| || || || ||||||||| | ||| ||||||| ||||| ||||||||||||| || ||||| |||||||||||||| ||||| ||
---ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
ttcatgtatgcatttt--ttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|||| || || | |||| || | || | || | || | || || |||| | || | | || ||| | |||||| || ||||| || || || ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||
ttcaagttcctatccaaacggacaccttgttgatattag-ctcgagttctatactttcat-tgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
-----ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
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gaaagactat-tatggaaacaatgctaatggtaacttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctc---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|22525826|gb|BU084637.1|BU084637EST: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG CGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
genomic: GTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaa ... tatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
- - -gtatgca
- - - - - - - - -tgcgccc
- - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt