Sequence
atgc intronic sequence ATGC exonic sequence...gtgccatttttgtccatagagtagtgaagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
Basic information
species | Glycine max |
transcript | GLYMA11G18900.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 4
gtgccatttttgtccatagagtagtgaag-atgccaatgtgat-atagt--tgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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--------------------gtagtgtgttatcctattgcgatcatggtactgatatttcattaggtggattctaactgttg---tcacacatgtaa--tgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 4
gtgccatttttgtccatagagtagtgaag-atgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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--------------------gtaatgcactgtcctaataataaacttatgattttaagtgtggtcgatgc---ttactgtcatgcacatatgtaat-gcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
gtgccat-ttttgtccata---gagtagtgaagatgccaatgtgatatagttgatct-atcttatggta-ggtttcagttacagaat-ttagtctttctg-gttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
gtgccat-ttttgtccatagagtagtg---aagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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gtattgcattgtgctgatacgatagcgattagcaaactatcaatatatacttcacccatc--acaat-gatgctaactatagca------cgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 4
gtgccatttttgtccatagagtagtgaagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtcttt----ctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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---gcattttaagatttcaatcaat-aatttatcattttatcgttctgcaactgtttcaataacaccattggtaacagccttctatgttttcttctcatcatagATGGCAGATCCTCTGACTGCATTGATGTATGCTGTCCAAGTCATGAATTTCCTCAAGACACTTATCATAAAGACACTACGAGAAAGAGAAGATTCAATGG
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtgccatttttg-----tccatagagtagtga-----agatgccaat-gtgatatagttga-----tctatcttatggtaggtttc-agttacag----------aatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
upper sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------gtgccatttttgtccatagag--tagtgaagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATACMapped 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|51344603|gb|CO985336.1|CO985336EST: AGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCAT ATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTC
genomic: AGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtgagttcca ... ctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
agttgat putative branch site (score: 5)
tctttct putative PPT
tatcttat 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgccatttttgtccatagagtagtgaagatgccaatgtgatatagttgatctatcttatggtaggtttcagttacagaatttagtctttctggttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG
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