Sequence
atgc intronic sequence ATGC exonic sequencegtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
Basic information
species | Glycine max |
transcript | GLYMA12G06980.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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-----------------------------------------gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
gtaattccttatcttttctccttggcaacatctcattgttgagggcaca-aacagtagaagttttgcactgccgttaa-ctaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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gtaacacttcatctttcactt------aaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacg--gtatttatcatctatgtctgt-----agAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattt-tcattttttttctct--------cagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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--------------------------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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---gtaagttgcattttctc------aggctctcgct--tcaactttctccctgtaa----tttgcatcaacatattctcattgtcctttattccttaaa----ttgtttttgtttcttctttgt-agAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctct-cagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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-----------------------gtcagttttctacttccctaaactca--ctgcatcactttt---------ttctttatccagtgattcctt--taagattctcattggcctgtttgtcatttgtagAAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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-------------------------------gtaacttttgtgttttttt----ttttaatcctgaacaaacttcaatgaatatgaagt--tttaatatg-tatgttgtttctttatattttggacagAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataa-ctcaat-gtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
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-------------------------aaggatgcgatgaaatgtagctctgagtgtag-----tagcatcactgaattccaagaagcttggatcttggtcataatctctgctttgctattcgtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAGMapped 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|213606684|gb|DB959073.1|DB959073EST: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTG
genomic: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattcctt ... tttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTG
EST:
gi|209703510|gb|BW656548.1|BW656548EST: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG AAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTG
genomic: GCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattcctt ... tttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
caataac putative branch site (score: 2)
tgcttattttcatttt putative PPT
atgcttattttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcagAAATACGCATTGCGAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATCGCTCAAGCAATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA