Sequence
atgc intronic sequence ATGC exonic sequencegtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
Basic information
species | Glycine max |
transcript | GLYMA12G27400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 5
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagttttttta-atgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-----------------------gcatgc-acttctgttcacctagatcttttacatgctcgtcttagtttgtgattgatatttattagtgatgctaaacttttgcttaatttgcttgtagACCATAGCAGTGATCCAAGCTGGCCATGGCCTTCTTCAGCTTGGCTCTTGCAAGATC
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 5
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-----------------gcaagggagttgtttgattcaccagccgaattttcatttgt---ctttataatcaatatagttttggtgacatttgtattttttttatctgctctg----cagACCATAGCTGTGATCCAAGCCGGGCATGGCCTCCTGCAGCTGGGCTCTTGCAAGATT
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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-------------------------------------------gtaaatataatcaaacttcttttggttatatactgttc---ttgatcttaccttaacagtgttt--tatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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------------gtaaaataa----agaacactaatcatatatgagaatgttcttgactttctt----gtttc--tcaagtcacctt------tgtaatcttttcttattgtacctacagACCATAGCTGTTATTCAAGCCGGACATGGCCTTTTACAACTTGGTTCTTGCAAGATT
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 5
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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gtcagaatcacagt-agtttgtggttttctattgttggtct--------ttgcgttatttgcattattgcttcttttctctgtcccttaattttgtcatctttgtatgtcccttgaccagACCATAGCTGTAATTCAAGCTGGCCATGGCCTTCTTCAACTCGGTTCCTGCAAGATT
upper sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05904 (Selaginella moellendorffii), 3'ss of exon 6
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatt-tattccattgc-cagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
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----------------------------------------------------------gtagct----atccggaattctctttcttcacgggctctaagaaccttgtataccatctcgcagACCATAGCTGTGATTCAAGCTGGGCACGGACTTCTCCAACTAGGATCCTGCAAGATCMapped 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|298172875|gb|HO019859.1|HO019859EST: CTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG ACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGC
genomic: CTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAGgtgagggaca ... ccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGC
EST:
gi|298177186|gb|HO027081.1|HO027081EST: CTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG ACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGC
genomic: CTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAGgtgagggaca ... ccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
tttattcc CT-rich tract
aatcatttcattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA