Sequence
atgc intronic sequence ATGC exonic sequence...tctactgcatgaacacaagcatcatgtatctgcatgattattaaacttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
Basic information
species | Glycine max |
transcript | GLYMA18G07480.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g63270.2 (Oryza sativa), 3'ss of exon 12
--tctactgcatgaacacaagcatcatgtatctgcatgattattaaacttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
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catatagtgagt-aatattaagataatctagatttgtaatccttacacaaatatttgattgtaattttgaattaaaatgtggacctccttgttcctc-tcagGTGGTGTTCATTCCCAACTACAATGTATCTGTGGCCGAGGTGCTCATTCCTGGGAGTGAACTGTCACAGCACATCAGTACCGCAGGCATGGAAGCAAGTG
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
---------------------------------------------------tctactgcatgaacacaagca-tcatgtatctgcatgattattaaacttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
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gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcattta---cttaaagtgttcttttcc--ttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 13
tctactgcatgaacacaagcatcatgtatctgcatgattattaaacttattcttagtgggg-aacaaaatctaaactgtttttattaaacttttttgtc-agGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
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gccaa-gcctga-tgcaaatgcaataaatcactgttctccttttattttccgaacatagcttgaagaagttttaactggttctaacgcatttgcttctccagGTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCCGGAAGTGAGCTATCTCAACACATCAGCACAGCAGGCATGGAGGCAAGTG
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 12
tctactgcatgaacacaagcatcatgtatctgcatgattattaaacttattctt--agtggggaacaaaatctaaactgtttttat---taaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
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-----tgtatgttttggctttttaagcttttttatattcagcaatcttttttttttagtatatgctacacttgctgatgcatccataactgtaaaaaaatttcagGTTGTTTTTGTTCCAAATTATAATGTGTCTGTGGCAGAGGTGCTTATTCCAGGAAGTGAGTTGTCACAGCACATCAGCACAGCTGGCATGGAAGCCAGTGMapped 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|18040420|gb|BM308714.1|BM308714EST: ATGTCGGTGCCGTCGTCAACAGTGACCCTGAGGTCAATAGCTACTTGAAG GTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA
genomic: ATGTCGGTGCCGTCGTCAACAGTGACCCTGAGGTCAATAGCTACTTGAAGgtaacttaat ... tttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
atctaaa putative branch site (score: 3)
cttttttgtc putative PPT
aacaaaatctaaactg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctactgcatgaacacaagcatcatgtatctgcatgattattaaacttattcttagtggggaacaaaatctaaactgtttttattaaacttttttgtcagGTTGTGTTTGTTCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - gcatgaa
- - - - - - - -caagcat
- - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - agtgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa