Sequence
atgc intronic sequence ATGC exonic sequencegtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgttatgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
Basic information
species | Glycine max |
transcript | GLYMA08G21830.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 4
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgttatgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
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------------------------------------------------------atcgtgaa--gctgattagatgccttgatactgagattcacttctgttacttccattttttgcactagttgtttcattacatcag---tgatacatggg--------------atgc-agGTGTCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCGGTCAAAAGAGTTGGTAGATGTGATGCTTTTGCTACAGAATACGATCTTGAAGCTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 4
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgttatgattgggggatttttgccaacatgc-cagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
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--------------------------------------------------------------------------gctgagtagctccttaaacattgagttaccttatctattctgtatttctgttatctgcatttgttgcttta-ggttactcattgtctgcctatggatatagGTGGCAGTGGGTGATGTTATATACATTGAAGCAAATAGTGGAGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgt-tatgattgggggatttttgccaacatgc--cagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
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---------------------------------------------------------------------------atcattagtttatagg--tctacttgcatgcttagattgttatttttttcttttattttttattttgtgtatggtttcattatttttcaatacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 4
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgtta--tgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
|| || || | || | || | || || || | | | || | | ||| |||| || || ||||| || |||||||| || || ||||| ||||| ||| | || || ||||||||||||||||| || || || ||||||||||| |
-------------------------------------------------------------------------------------------------------------------gtgatggtttc--cgacggttttgctctttgctggttttgaaactgttatc-----gtcagGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACCGAATTCGACCTTGAAGCGG
upper sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 4
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgtta--tgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
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-------------------------------------------------------------------------------------------------------------------gtgatggtttc--caacggttttgctctttgctggttttgaaactgttatc-----gtcagGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACTGAATTCGACCTTGAAGCGGMapped 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|193576011|gb|FK532156.1|FK532156EST: ATATATGATGCCTTGATTAAGGAAAAG ATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
genomic: ATATATGATGCCTTGATTAAGGAAAAGgtgaggtctc ... aacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
EST:
gi|151406331|gb|EV276146.1|EV276146EST: AGCAACTCAAGTTGGATCCTACCATATATGATGCCTTGATTAAGGAAAAG ATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
genomic: AGCAACTCAAGTTGGATCCTACCATATATGATGCCTTGATTAAGGAAAAGgtgaggtctc ... aacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
EST:
gi|208298810|gb|GE091421.1|GE091421EST: AGCAACTCAAGTTGGATCCTACCATATATAATGCCTTGATTAAGGAAAAG ATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
genomic: AGCAACTCAAGTTGGATCCTACCATATATGATGCCTTGATTAAGGAAAAGgtgaggtctc ... aacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgtgtcaacaaatctgatgttatgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
atctgat putative branch site (score: 4)
ttatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggtctctaatttcctcttgttctgtgtgtgctccattgtgtaactaagatattgcaagttataaatttcttttctttattttgtatgaagctgttttagttttgaagttgtgtaatatttgtgtcaacaaatctgatgttatgattgggggatttttgccaacatgccagATAGCTGTTGGCGATGTTATATACATTGAGGCAAATAGCGGGGCTGTAAAAAGGGTGGGTCGAAGTGATGCTTTCGCTACAGAGTTTGACCTTGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG