Sequence
atgc intronic sequence ATGC exonic sequence...atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
Basic information
species | Glycine max |
transcript | GLYMA07G38140.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
-atatatatatatata-tatatatatacatggggttggttcatatctcagcttactttt----atgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC------
| | | || || ||| | |||| | | | ||| | || ||| |||||| | |||| | | | ||| ||||| |||| | || || | ||||||||||||||||| || |||||||| || |||||||||||||| ||| | ||||| | | |||||| |||| ||
ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatt---tatttatatctta---cagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGT------CTCTTTGGTTTCTACAAATCACA
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
----------------------atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactctta----ttacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
| | | || | | || | |||| | || | | |||| || | ||| || | | | | | || || || |||| | | |||| |||||||||||||||| ||||||||||| || ||||| ||||| || ||| | ||||| | || || ||||||||||||| ||||
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgat-ccgccacaatcagaaacatactcctagaac--aatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
------------------atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactctta----ttacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
| | | || | | || | |||| | || | | |||| || | ||| || | | | | | || || || |||| | | |||| |||||||||||||||| ||||||||||| || ||||| ||||| || ||| | ||||| | || || ||||||||||||| ||||
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgat-ccgccacaatcagaaacatactcctagaac--aatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
atatatatatatatatatatatatacatggggttggttcatatctcagcttactttt--atgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
| | | || | | | | | ||| ||||| | || |||| |||| || || | |||| |||||| | | | | | || |||||||||||||||||||||||||| ||||| ||||| || ||| ||||||| | | || || |||| | |||||
gagtcttatcagccatg-gtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttc-cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
--------------------------------------atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgta-----------gtaatggttgcttaactcttat-tacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
|| || | | | | ||| | | |||| | |||| | | || | ||| | || | || || | |||| | |||||| | | | || |||| |||||||||||||||||||||||||| ||||| ||||| || ||| | || || | || |||| ||| ||||| | |||
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttg-tagtaatggttgcttaactcttatta----cagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
| ||| || | || | ||| || | || | ||| | | | | | || || | | | || | | ||||||||| ||||| | ||| || |||| ||||||||||| ||||| || || ||||||||||||||||| ||| | |||||| | || |||| | || || |
--gtgccatagcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtctta-atcttgtagtaatggttgcttaactcttatta----cagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
||| ||| || | || | ||| || | || | ||| | | | | | | || | | | || | | ||||||||| ||||| | ||| || |||| ||||||||||| ||||| || || ||||||||||||||||| ||| | |||||| | || |||| | || || | |
----ccata-gcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC
upper sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
-----atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
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tttcatcatgtggctccatataattttgttgatcaagttggttctgatacttg-tagtttgtagattttga--ttgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCACMapped 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|298172062|gb|HO021654.1|HO021654EST: GGGGAATTCCAGTTCCAGATTCAAATGCTGAGATGCAAGCAAATATTGAT AGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTT
genomic: GGGGAATTCCAGTTCCAGATTCAAATGCTGAGATGCAAGCAAATATTGATgtatgtcaga ... cttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTT
EST:
gi|207806240|gb|GD778717.1|GD778717EST: GGGGAATTCCAGTTCCAGATTCAAATGCTGAGATGCAAGCAAATATTGAT AGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTT
genomic: GGGGAATTCCAGTTCCAGATTCAAATGCTGAGATGCAAGCAAATATTGATgtatgtcaga ... cttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcttacttttatgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
gcttaac putative branch site (score: 3)
ctcttatt CT-rich tract
ttttatgtcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - -gggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc