Sequence
atgc intronic sequence ATGC exonic sequence...cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
Basic information
species | Glycine max |
transcript | GLYMA08G13370.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
cactgaattagtgaaacagattaaata---tgtatatttcattt--gtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgttt-cagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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-----ctttcctaaaataaattcattattatgtttaccataattccatggtagaactttgtgagct-caacagttctcatctgccttttatgcttcttatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 1
-----cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
|| || | || | | | | | |||| || || | | | || | | | | || | ||| |||| ||| | ||||| || || ||| | ||||| || ||||| ||||| ||||| || || || || || |||||||| ||||||||||||||||||||||||||||| |
gccatttctaaa--aactaagcctactgatt-tgta-atcacactgagaacaacttttg-tatgttagtaatcacttcatctacctgttatttaattttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTACAATAACCCGCAAGAAACTTACAACTATTACAGCCTCCCATTTTGTCAGC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 1
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctg--tttttaaaaga----atgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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--tttaggtgatattttggcctac---tgtgtattttggaggaagaatgtgtttgtctggtgctttggaacatttacgatgtgtcgtgttcttcgctttgtgt-agTACCAATCGGAGGAGAAGGTTATGCTCTGGGTGAACAAGGTTGGCCCGTACAACAACCCACAGGAAACTTACAACTACTACAGCCTTCCGTTTTGCCATC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 1
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaa-gtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| | |||| || | | | | || |||| || || | | ||| | | | | | | || | ||||| || || || |||||||| ||||||||||| |||||||| ||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| |
-gattgctgcttgaatgttgttttccttatgcttcctacatgctgtgcaaatatgttccgtactcaaaatttctcatccctttcaatgcttcttaatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAACAATCCTCAAGAAACTTACAACTACTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
-cactgaattagtgaaacagattaaatatgtatatttcat-ttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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ttgctgattgagtgctgtt--ttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 1
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaactt----ctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| | | | | || | || || | | || || | | | || || | || | ||| | || ||| ||| |||| ||| | || || || | || ||||||||||| |||||||| || |||||||| || || ||||||||||| ||||||||||||||||| |||
-gcccagc--gctagataggatttttacgtttttgccaacaa-gctgtctaatcgttctcatccatgcgctttctttctttctgctgctgtttgtttattttagTACCAAGCAGCGGAGCCTGTGACGCTCTGGGTGAACAAGGTTGGTCCGTACAACAATCCGCAGGAGACATACAACTACTACAGCCTCCCATTTTGCCATG
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 1
-------cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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ttgctgtcttttcagaatttacctgcactgaatttaactatgacgataatgcctttacctactaaatcattgcagcttataa-------tatttttcttatgtgcagTATAAAACAGAAGAACCTGTTAAGCTATGGGTAAACAAGGTTGGGCCTTACAATAACCCTCAAGAAACTTACAACTATTACAGTCTCCCGTTTTGTCAAC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttg-----tttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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----gaattt-tggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
---cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
||||| | || | | | | | | | || | | | | | | |||| | | | | | | | | ||| || | | |||||||| ||||| | || | || ||||| ||||||||||||||||| || |||||||||||||| |||||||| | |||||| ||||||||||| |
agacactggctctgttacagtattcatgaa---acacttaactgggaaatatgtgacttaaacataatattgtataaggaaatcatttttgtttctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
-cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgttt--cagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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atgctacttctgt-acttactttctgtaagta-gctcaaattacagctcttgcttttgttccagatgcactttgttaacagt-tttttaattttgtcttgcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC
upper sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 1
cactgaattagtgaaacagattaa-atatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
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ggaacgatcggggtgccatgtcagcacctgcacatggc-tttgtgatgacgaactgggccgcggttgtgatgggtgaggtccgtgtgttgtgagtgtgcagTATGGCAAAGGGGATCCGGTGATGCTGTGGGTGAACAAAGTGGGGCCTTACAACAATCCGCAAGAGACGTACAACTACTACAGTCTGCCGTTTTGCAGTCMapped 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|18690803|gb|BM519651.1|BM519651EST: TTTTCTCTCTCTTCCTTTCTTCCGCCTTCGCTTCAGACTCAGATCACAAG TATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTAT
genomic: TTTTCTCTCTCTTCCTTTCTTCCGCCTTCGCTTCAGACTCAGATCACAAGgtaattcctc ... tttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
ttttattttgtttc CT-rich tract
ttctgtttttaaaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
cactgaa
- - - - - - gaaacaga
- - - - - - - - - - - - - - - - - - - - tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - agtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa