Sequence
atgc intronic sequence ATGC exonic sequence...gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
Basic information
species | Glycine max |
transcript | GLYMA14G21190.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
gctacaataagattcatatttgtt-ttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttt--tgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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---cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 7
----gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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gcttgcgaaattaaagtccatatttgtatacaccaccgtattgtgtaaagcatttttaatttgtaacttttg---tgtatcgtggt-attcccttttaattcagAGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 7
gctacaataagattca--tatttgttttgtaatt-tgtttttcattcattttttcatcttcatggtctttgc-tttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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----gagttgatttcttctacttgtttcaacattgtgccagtgaatcattctctgttcattattacatgcatatgtgaatgcaattgtccttttccatttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
gctacaat-aagattcatatttgttttgtaatttgtttttcattcattttttcatc-ttcatggtctttgctt-tgaat-cttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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---gtaattggggctagcccttgcattttgaga-gcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
---------gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
| | |||||| | | || || || ||| | | ||| || | |||| || | || | ||| ||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| || |||
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaat---------tgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18240 (Selaginella moellendorffii), 3'ss of exon 6
gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgc-agGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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---------------------------------gtaccgtgttcacttacaaaacaaca----ctttgat--gatttgttttctctctc-tgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
upper sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgc-agGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
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---------------------------------gtaccgtgttcacttacaaaacaaca----ctttgatc--attcgttttctctctc-tgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGMapped 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|192334327|gb|FK025532.1|FK025532EST: GGATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG GCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATG
genomic: GAATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaagtattt ... tgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATG
EST:
gi|208136700|gb|GD939674.1|GD939674EST: GAATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG GCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATG
genomic: GAATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaagtattt ... tgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
aatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG
- - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatctc