Sequence
atgc intronic sequence ATGC exonic sequence...gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
Basic information
species | Glycine max |
transcript | GLYMA08G08730.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g44040.3 (Oryza sativa), 3'ss of exon 10
----gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
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tggcaatgatggctgtgcacgtccaaagtttcagttttgtgcttacatatcaagatgttttgtctctttc-gattgtcactgaa---ttcttatatgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 8
------------------------------------------------------------------------------------------gatcaagaacaaag-----------ataggaaaagattat--aatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
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gtatgactcttgagttacctctacgtttttccctaattattgaaggtgcttccagttcactaaccttgtggtaatagcatgttggtagaagatcaactccaatgtttcttctcatatagcagtagtttattcaactgaactaaaaatgctgctcaaatgtctttgcttcgccacattgtgaccaagcttctttt-----gcagGTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTT
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 14
gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgca---tacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
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---------------------------------gtttgttttctgtgacttaatcttttcc---tggaagcgtatttgttaaatcaaagacaccaattttcagATCAAACATGCCTGACGGGCAACCAAAATGGCTTCTCTCTATTATTCCGGGATACCCTATGCTCAATTTCATGCTGACAACTGCTATATACGTCCTT
upper sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtac-ttgataatttcc---tctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
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----ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTAMapped 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|21601984|gb|BQ612315.1|BQ612315EST: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
EST:
gi|14516286|gb|BI094958.1|BI094958EST: GGCAAGATTACTTTGGATACATACATTTCCCAGTTTCATATTTGGTTAAG GTCTAACATGCCAAACGGACAGCCCAAGTGGCTTTTTTCTCTTATCCCGGA
genomic: GGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAGgtgtgtatgc ... ttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
acttgat putative branch site (score: 5)
tttcctctttgcat putative PPT
ttgataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtacttgataatttcctctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
- - aagaacaa
- - - - - - - - -ggaaaaga
- - - - - - - - - - - - - - - - - - - -aacgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgtac